Differential Phytotoxic Impact of Plant Mediated Silver Nanoparticles (AgNPs) and Silver Nitrate (AgNO3) on Brassica sp.

PubMed Central

Vishwakarma, Kanchan; Shweta; Upadhyay, Neha; Singh, Jaspreet; Liu, Shiliang; Singh, Vijay P.; Prasad, Sheo M.; Chauhan, Devendra K.; Tripathi, Durgesh K.; Sharma, Shivesh

2017-01-01

Continuous formation and utilization of nanoparticles (NPs) have resulted into significant discharge of nanosized particles into the environment. NPs find applications in numerous products and agriculture sector, and gaining importance in recent years. In the present study, silver nanoparticles (AgNPs) were biosynthesized from silver nitrate (AgNO3) by green synthesis approach using Aloe vera extract. Mustard (Brassica sp.) seedlings were grown hydroponically and toxicity of both AgNP and AgNO3 (as ionic Ag+) was assessed at various concentrations (1 and 3 mM) by analyzing shoot and root length, fresh mass, protein content, photosynthetic pigments and performance, cell viability, oxidative damage, DNA degradation and enzyme activities. The results revealed that both AgNPs and AgNO3 declined growth of Brassica seedlings due to enhanced accumulation of AgNPs and AgNO3 that subsequently caused severe inhibition in photosynthesis. Further, the results showed that both AgNPs and AgNO3 induced oxidative stress as indicated by histochemical staining of superoxide radical and hydrogen peroxide that was manifested in terms of DNA degradation and cell death. Activities of antioxidants, i.e., ascorbate peroxidase (APX) and catalase (CAT) were inhibited by AgNPs and AgNO3. Interestingly, damaging impact of AgNPs was lesser than AgNO3 on Brassica seedlings which was due to lesser accumulation of AgNPs and better activities of APX and CAT, which resulted in lesser oxidative stress, DNA degradation and cell death. The results of the present study showed differential impact of AgNPs and AgNO3 on Brassica seedlings, their mode of action, and reasons for their differential impact. The results of the present study could be implied in toxicological research for designing strategies to reduce adverse impact of AgNPs and AgNO3 on crop plants. PMID:29075270

Deletion of a Stay-Green Gene Associates with Adaptive Selection in Brassica napus.

PubMed

Qian, Lunwen; Voss-Fels, Kai; Cui, Yixin; Jan, Habib U; Samans, Birgit; Obermeier, Christian; Qian, Wei; Snowdon, Rod J

2016-12-05

Chlorophyll levels provide important information about plant growth and physiological plasticity in response to changing environments. The stay-green gene NON-YELLOWING 1 (NYE1) is believed to regulate chlorophyll degradation during senescence, concomitantly affecting the disassembly of the light-harvesting complex and hence indirectly influencing photosynthesis. We identified Brassica napus accessions carrying an NYE1 deletion associated with increased chlorophyll content, and with upregulated expression of light-harvesting complex and photosynthetic reaction center (PSI and PSII) genes. Comparative analysis of the seed oil content of accessions with related genetic backgrounds revealed that the B. napus NYE1 gene deletion (bnnye1) affected oil accumulation, and linkage disequilibrium signatures suggested that the locus has been subject to artificial selection by breeding in oilseed B. napus forms. Comparative analysis of haplotype diversity groups (haplogroups) between three different ecotypes of the allopolyploid B. napus and its A-subgenome diploid progenitor, Brassica rapa, indicated that introgression of the bnnye1 deletion from Asian B. rapa into winter-type B. napus may have simultaneously improved its adaptation to cooler environments experienced by autumn-sown rapeseed. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

Brassica rapa plants adapted to microgravity with reduced photosystem I and its photochemical activity

NASA Technical Reports Server (NTRS)

Jiao, Shunxing; Hilaire, Emmanuel; Paulsen, Avelina Q.; Guikema, James A.

2004-01-01

The photosynthetic apparatus contains several protein complexes, many of which are regulated by environmental conditions. In this study, the influences of microgravity on PSI and PSII in Brassica rapa plants grown aboard the space shuttle were examined. We found that Brassica plants grown in space had a normal level of growth relative to controls under similar conditions on Earth. Upon return to Earth, cotyledons were harvested and thylakoid membranes were isolated. Analysis of chlorophyll contents showed that the Chl a/b ratio (3.5) in flight cotyledons was much higher than a ratio of 2.42 in the ground controls. The flight samples also had a reduction of PSI complexes and a corresponding 30% decrease of PSI photochemical activity. Immunoblotting showed that the reaction centre polypeptides of PSI were more apparently decreased (e.g. by 24-33% for PsaA and PsaB, and 57% for PsaC) than the light-harvesting complexes. In comparison, the accumulation of PSII complex was less affected in microgravity, thus only a slight reduction in D1, D2 and LHCII was observed in protein blots. However, there was a 32% decrease of OEC1 in the flight samples, indicating a defective OEC subcomplex. In addition, an average 54% increase of the 54 kDa CF1-beta isoform was found in the flight samples, suggesting that space-grown plants suffered from certain stresses, consistent with implications of the increased Chl a/b ratio. Taken together, the results demonstrated that Brassica plants can adapt to spaceflight microgravity, but with significant alterations in chloroplast structures and photosynthetic complexes, and especially reduction of PSI and its activity.

Taste detection of the non-volatile isothiocyanate moringin results in deterrence to glucosinolate-adapted insect larvae.

PubMed

Müller, Caroline; van Loon, Joop; Ruschioni, Sara; De Nicola, Gina Rosalinda; Olsen, Carl Erik; Iori, Renato; Agerbirk, Niels

2015-10-01

Isothiocyanates (ITCs), released from Brassicales plants after hydrolysis of glucosinolates, are known for their negative effects on herbivores but mechanisms have been elusive. The ITCs are initially present in dissolved form at the site of herbivore feeding, but volatile ITCs may subsequently enter the gas phase and all ITCs may react with matrix components. Deterrence to herbivores resulting from topically applied volatile ITCs in artificial feeding assays may hence lead to ambiguous conclusions. In the present study, the non-volatile ITC moringin (4-(α-L-rhamnopyranosyloxy)benzyl ITC) and its glucosinolate precursor glucomoringin were examined for effects on behaviour and taste physiology of specialist insect herbivores of Brassicales. In feeding bioassays, glucomoringin was not deterrent to larvae of Pieris napi (Lepidoptera: Pieridae) and Athalia rosae (Hymenoptera: Tenthredinidae), which are adapted to glucosinolates. Glucomoringin stimulated feeding of larvae of the related Pieris brassicae (Lepidoptera: Pieridae) and also elicited electrophysiological activity from a glucosinolate-sensitive gustatory neuron in the lateral maxillary taste sensilla. In contrast, the ITC moringin was deterrent to P. napi and P. brassicae at high levels and to A. rosae at both high and low levels when topically applied to cabbage leaf discs (either 12, 120 or 1200 nmol moringin per leaf disc of 1cm diameter). Survival of A. rosae was also significantly reduced when larvae were kept on leaves treated with moringin for several days. Furthermore, moringin elicited electrophysiological activity in a deterrent-sensitive neuron in the medial maxillary taste sensillum of P. brassicae, providing a sensory mechanism for the deterrence and the first known ITC taste response of an insect. In simulated feeding assays, recovery of moringin was high, in accordance with its non-volatile nature. Our results demonstrate taste-mediated deterrence of a non-volatile, natural ITC to glucosinolate-adapted

Transcriptome analysis of Brassica juncea var. tumida Tsen responses to Plasmodiophora brassicae primed by the biocontrol strain Zhihengliuella aestuarii.

PubMed

Luo, Yuanli; Dong, Daiwen; Su, Yu; Wang, Xuyi; Peng, Yumei; Peng, Jiang; Zhou, Changyong

2018-05-01

Mustard clubroot, caused by Plasmodiophora brassicae, is a serious disease that affects Brassica juncea var. tumida Tsen, a mustard plant that is the raw material for a traditional fermented food manufactured in Chongqing, China. In our laboratory, we screened the antagonistic bacteria Zhihengliuella aestuarii against P. brassicae. To better understand the biocontrol mechanism, three transcriptome analyses of B. juncea var. tumida Tsen were conducted using Illumina HiSeq 4000, one from B. juncea only inoculated with P. brassicae (P), one inoculated with P. brassica and the biocontrol agent Z. aestuarii at the same time (P + B), and the other was the control (H), in which P. brassicae was replaced by sterile water. A total of 19.94 Gb was generated by Illumina HiSeq sequencing. The sequence data were de novo assembled, and 107,617 unigenes were obtained. In total, 5629 differentially expressed genes between biocontrol-treated (P + B) and infected (P) samples were assigned to 126 KEGG pathways. Using multiple testing corrections, 20 pathways were significantly enriched with Qvalue ≤ 0.05. The resistance-related genes, involved in the production of pathogenesis-related proteins, pathogen-associated molecular pattern-triggered immunity, and effector-triggered immunity signaling pathways, calcium influx, salicylic acid pathway, reactive oxygen intermediates, and mitogen-activated protein kinase cascades, and cell wall modification, were obtained. The various defense responses induced by the biocontrol strain combatted the P. brassicae infection. The genes and pathways involved in plant resistance were induced by a biocontrol strain. The transcriptome data explained the molecular mechanism of the potential biocontrol strain against P. brassicae. The data will also serve as an important public information platform to study B. juncea var. tumida Tsen and will be useful for breeding mustard plants resistant to P. brassicae.

Functional analysis and tissue-differential expression of four FAD2 genes in amphidiploid Brassica napus derived from Brassica rapa and Brassica oleracea.

PubMed

Lee, Kyeong-Ryeol; In Sohn, Soo; Jung, Jin Hee; Kim, Sun Hee; Roh, Kyung Hee; Kim, Jong-Bum; Suh, Mi Chung; Kim, Hyun Uk

2013-12-01

Fatty acid desaturase 2 (FAD2), which resides in the endoplasmic reticulum (ER), plays a crucial role in producing linoleic acid (18:2) through catalyzing the desaturation of oleic acid (18:1) by double bond formation at the delta 12 position. FAD2 catalyzes the first step needed for the production of polyunsaturated fatty acids found in the glycerolipids of cell membranes and the triacylglycerols in seeds. In this study, four FAD2 genes from amphidiploid Brassica napus genome were isolated by PCR amplification, with their enzymatic functions predicted by sequence analysis of the cDNAs. Fatty acid analysis of budding yeast transformed with each of the FAD2 genes showed that whereas BnFAD2-1, BnFAD2-2, and BnFAD2-4 are functional enzymes, and BnFAD2-3 is nonfunctional. The four FAD2 genes of B. napus originated from synthetic hybridization of its diploid progenitors Brassica rapa and Brassica oleracea, each of which has two FAD2 genes identical to those of B. napus. The BnFAD2-3 gene of B. napus, a nonfunctional pseudogene mutated by multiple nucleotide deletions and insertions, was inherited from B. rapa. All BnFAD2 isozymes except BnFAD2-3 localized to the ER. Nonfunctional BnFAD2-3 localized to the nucleus and chloroplasts. Four BnFAD2 genes can be classified on the basis of their expression patterns. © 2013.

Comparative proteomic study on Brassica hexaploid and its parents provides new insights into the effects of polyploidization.

PubMed

Shen, Yanyue; Zhang, Yu; Zou, Jun; Meng, Jinling; Wang, Jianbo

2015-01-01

Polyploidy has played an important role in promoting plant evolution through genomic merging and doubling. Although genomic and transcriptomic changes have been observed in polyploids, the effects of polyploidization on proteomic divergence are poorly understood. In this study, we reported quantitative analysis of proteomic changes in leaves of Brassica hexaploid and its parents using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with mass spectrometry. A total of 2044 reproducible proteins were quantified by at least two unique peptides. We detected 452 proteins differentially expressed between Brassica hexaploid and its parents, and 100 proteins were non-additively expressed in Brassica hexaploid, which suggested a trend of non-additive protein regulation following genomic merger and doubling. Functional categories of cellular component biogenesis, immune system process, and response to stimulus, were significantly enriched in non-additive proteins, probably providing a driving force for variation and adaptation in allopolyploids. In particular, majority of the total 452 differentially expressed proteins showed expression level dominance of one parental expression, and there was an expression level dominance bias toward the tetraploid progenitor. In addition, the percentage of differentially expressed proteins that matched previously reported differentially genes were relatively low. This study aimed to get new insights into the effects of polyploidization on proteomic divergence. Using iTRAQ LC-MS/MS technology, we identified 452 differentially expressed proteins between allopolyploid and its parents which involved in response to stimulus, multi-organism process, and immune system process, much more than previous studies using 2-DE coupled with mass spectrometry technology. Therefore, our manuscript represents the most comprehensive analysis of protein profiles in allopolyploid and its parents, which will lead to a better understanding of

Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas.

PubMed

Sri, Tanu; Mayee, Pratiksha; Singh, Anandita

2015-09-01

Whole genome sequence analyses allow unravelling such evolutionary consequences of meso-triplication event in Brassicaceae (∼14-20 million years ago (MYA)) as differential gene fractionation and diversification in homeologous sub-genomes. This study presents a simple gene-centric approach involving microsynteny and natural genetic variation analysis for understanding SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1) homeolog evolution in Brassica. Analysis of microsynteny in Brassica rapa homeologous regions containing SOC1 revealed differential gene fractionation correlating to reported fractionation status of sub-genomes of origin, viz. least fractionated (LF), moderately fractionated 1 (MF1) and most fractionated (MF2), respectively. Screening 18 cultivars of 6 Brassica species led to the identification of 8 genomic and 27 transcript variants of SOC1, including splice-forms. Co-occurrence of both interrupted and intronless SOC1 genes was detected in few Brassica species. In silico analysis characterised Brassica SOC1 as MADS intervening, K-box, C-terminal (MIKC(C)) transcription factor, with highly conserved MADS and I domains relative to K-box and C-terminal domain. Phylogenetic analyses and multiple sequence alignments depicting shared pattern of silent/non-silent mutations assigned Brassica SOC1 homologs into groups based on shared diploid base genome. In addition, a sub-genome structure in uncharacterised Brassica genomes was inferred. Expression analysis of putative MF2 and LF (Brassica diploid base genome A (AA)) sub-genome-specific SOC1 homeologs of Brassica juncea revealed near identical expression pattern. However, MF2-specific homeolog exhibited significantly higher expression implying regulatory diversification. In conclusion, evidence for polyploidy-induced sequence and regulatory evolution in Brassica SOC1 is being presented wherein differential homeolog expression is implied in functional diversification.

[Morphological and biochemical adaptations to feeding in some herbivorous gastropods].

PubMed

Aliakrinskaia, O I

2005-01-01

Diet and feeding modes as well as morphological and biochemical adaptations to feeding are analyzed in herbivorous mollusks. The content of hemoglobin in radular tissues and weight properties of the radula are evaluated for different modes of feeding.

Tracing the Transcriptomic Changes in Synthetic Trigenomic allohexaploids of Brassica Using an RNA-Seq Approach

PubMed Central

Zhao, Qin; Zou, Jun; Meng, Jinling; Mei, Shiyong; Wang, Jianbo

2013-01-01

Polyploidization has played an important role in plant evolution and speciation, and newly formed allopolyploids have experienced rapid transcriptomic changes. Here, we compared the transcriptomic differences between a synthetic Brassica allohexaploid and its parents using a high-throughput RNA-Seq method. A total of 35,644,409 sequence reads were generated, and 32,642 genes were aligned from the data. Totals of 29,260, 29,060, and 29,697 genes were identified in Brassica rapa , Brassica carinata , and Brassica allohexaploid, respectively. We compared 7,397 differentially expressed genes (DEGs) between Brassica hexaploid and its parents, as well as 2,545 nonadditive genes of Brassica hexaploid. We hypothesized that the higher ploidy level as well as secondary polyploidy might have influenced these changes. The majority of the 3,184 DEGs between Brassica hexaploid and its paternal parent, B . rapa , were involved in the biosynthesis of secondary metabolites, plant–pathogen interactions, photosynthesis, and circadian rhythm. Among the 2,233 DEGs between Brassica hexaploid and its maternal parent, B . carinata , several played roles in plant–pathogen interactions, plant hormone signal transduction, ribosomes, limonene and pinene degradation, photosynthesis, and biosynthesis of secondary metabolites. There were more significant differences in gene expression between the allohexaploid and its paternal parent than between it and its maternal parent, possibly partly because of cytoplasmic and maternal effects. Specific functional categories were enriched among the 2,545 nonadditive genes of Brassica hexaploid compared with the additive genes; the categories included response to stimulus, immune system process, cellular process, metabolic process, rhythmic process, and pigmentation. Many transcription factor genes, methyltransferases, and methylation genes showed differential expression between Brassica hexaploid and its parents. Our results demonstrate that the

CANOLA CROP TAKES UP SELENIUM PROVIDES BIOFUEL AND FEED SUPPLEMENT

USDA-ARS?s Scientific Manuscript database

Many of the Brassica plant taxi that are candidates for phytoremediation of selenium also produce products that be used for refining into biodiesel, as well as selenium enriched animal feeds. These include canola (Brassica napus) that is planted in the Westside soils of central California (Oxalis si...

Salt-stress-responsive chloroplast proteins in Brassica juncea genotypes with contrasting salt tolerance and their quantitative PCR analysis.

PubMed

Yousuf, Peerzada Yasir; Ahmad, Altaf; Aref, Ibrahim M; Ozturk, Munir; Hemant; Ganie, Arshid Hussain; Iqbal, Muhammad

2016-11-01

Brassica juncea is mainly cultivated in the arid and semi-arid regions of India where its production is significantly affected by soil salinity. Adequate knowledge of the mechanisms underlying the salt tolerance at sub-cellular levels must aid in developing the salt-tolerant plants. A proper functioning of chloroplasts under salinity conditions is highly desirable to maintain crop productivity. The adaptive molecular mechanisms offered by plants at the chloroplast level to cope with salinity stress must be a prime target in developing the salt-tolerant plants. In the present study, we have analyzed differential expression of chloroplast proteins in two Brassica juncea genotypes, Pusa Agrani (salt-sensitive) and CS-54 (salt-tolerant), under the effect of sodium chloride. The chloroplast proteins were isolated and resolved using 2DE, which facilitated identification and quantification of 12 proteins that differed in expression in the salt-tolerant and salt-sensitive genotypes. The identified proteins were related to a variety of chloroplast-associated molecular processes, including oxygen-evolving process, PS I and PS II functioning, Calvin cycle and redox homeostasis. Expression analysis of genes encoding differentially expressed proteins through real time PCR supported our findings with proteomic analysis. The study indicates that modulating the expression of chloroplast proteins associated with stabilization of photosystems and oxidative defence plays imperative roles in adaptation to salt stress.

Difference in root K+ retention ability and reduced sensitivity of K+-permeable channels to reactive oxygen species confer differential salt tolerance in three Brassica species

PubMed Central

Chakraborty, Koushik; Bose, Jayakumar; Shabala, Lana; Shabala, Sergey

2016-01-01

Brassica species are known to possess significant inter and intraspecies variability in salinity stress tolerance, but the cell-specific mechanisms conferring this difference remain elusive. In this work, the role and relative contribution of several key plasma membrane transporters to salinity stress tolerance were evaluated in three Brassica species (B. napus, B. juncea, and B. oleracea) using a range of electrophysiological assays. Initial root growth assay and viability staining revealed that B. napus was most tolerant amongst the three species, followed by B. juncea and B. oleracea. At the mechanistic level, this difference was conferred by at least three complementary physiological mechanisms: (i) higher Na+ extrusion ability from roots resulting from increased expression and activity of plasma membrane SOS1-like Na+/H+ exchangers; (ii) better root K+ retention ability resulting from stress-inducible activation of H+-ATPase and ability to maintain more negative membrane potential under saline conditions; and (iii) reduced sensitivity of B. napus root K+-permeable channels to reactive oxygen species (ROS). The last two mechanisms played the dominant role and conferred most of the differential salt sensitivity between species. Brassica napus plants were also more efficient in preventing the stress-induced increase in GORK transcript levels and up-regulation of expression of AKT1, HAK5, and HKT1 transporter genes. Taken together, our data provide the mechanistic explanation for differential salt stress sensitivity amongst these species and shed light on transcriptional and post-translational regulation of key ion transport systems involved in the maintenance of the root plasma membrane potential and cytosolic K/Na ratio as a key attribute for salt tolerance in Brassica species. PMID:27340231

Brassica ASTRA: an integrated database for Brassica genomic research.

PubMed

Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

2005-01-01

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

Difference in root K+ retention ability and reduced sensitivity of K+-permeable channels to reactive oxygen species confer differential salt tolerance in three Brassica species.

PubMed

Chakraborty, Koushik; Bose, Jayakumar; Shabala, Lana; Shabala, Sergey

2016-08-01

Brassica species are known to possess significant inter and intraspecies variability in salinity stress tolerance, but the cell-specific mechanisms conferring this difference remain elusive. In this work, the role and relative contribution of several key plasma membrane transporters to salinity stress tolerance were evaluated in three Brassica species (B. napus, B. juncea, and B. oleracea) using a range of electrophysiological assays. Initial root growth assay and viability staining revealed that B. napus was most tolerant amongst the three species, followed by B. juncea and B. oleracea At the mechanistic level, this difference was conferred by at least three complementary physiological mechanisms: (i) higher Na(+) extrusion ability from roots resulting from increased expression and activity of plasma membrane SOS1-like Na(+)/H(+) exchangers; (ii) better root K(+) retention ability resulting from stress-inducible activation of H(+)-ATPase and ability to maintain more negative membrane potential under saline conditions; and (iii) reduced sensitivity of B. napus root K(+)-permeable channels to reactive oxygen species (ROS). The last two mechanisms played the dominant role and conferred most of the differential salt sensitivity between species. Brassica napus plants were also more efficient in preventing the stress-induced increase in GORK transcript levels and up-regulation of expression of AKT1, HAK5, and HKT1 transporter genes. Taken together, our data provide the mechanistic explanation for differential salt stress sensitivity amongst these species and shed light on transcriptional and post-translational regulation of key ion transport systems involved in the maintenance of the root plasma membrane potential and cytosolic K/Na ratio as a key attribute for salt tolerance in Brassica species. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks

PubMed Central

Börner, Andreas

2018-01-01

Cauliflower (Brassica oleracea var. botrytis) is an important vegetable crop for human nutrition. We characterized 192 cauliflower accessions from the USDA and IPK genebanks with genotyping by sequencing (GBS). They originated from 26 different countries and represent about 44% of all cauliflower accessions in both genebanks. The analysis of genetic diversity revealed that accessions formed two major groups that represented the two genebanks and were not related to the country of origin. This differentiation was robust with respect to the analysis methods that included principal component analysis, ADMIXTURE and neighbor-joining trees. Genetic diversity was higher in the USDA collection and significant phenotypic differences between the two genebanks were found in three out of six traits investigated. GBS data have a high proportion of missing data, but we observed that the exclusion of single nucleotide polymorphisms (SNPs) with missing data or the imputation of missing SNP alleles produced very similar results. The results indicate that the composition and type of accessions have a strong effect on the structure of genetic diversity of ex situ collections, although regeneration procedures and local adaptation to regeneration conditions may also contribute to a divergence. Fst-based outlier tests of genetic differentiation identified only a small proportion (<1%) of SNPs that are highly differentiated between the two genebanks, which indicates that selection during seed regeneration is not a major cause of differentiation between genebanks. Seed regeneration procedures of both genebanks do not result in different levels of genetic drift and loss of genetic variation. We therefore conclude that the composition and type of accessions mainly influence the level of genetic diversity and explain the strong genetic differentiation between the two ex situ collections. In summary, GBS is a useful method for characterizing genetic diversity in cauliflower genebank material

Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks.

PubMed

Yousef, Eltohamy A A; Müller, Thomas; Börner, Andreas; Schmid, Karl J

2018-01-01

Cauliflower (Brassica oleracea var. botrytis) is an important vegetable crop for human nutrition. We characterized 192 cauliflower accessions from the USDA and IPK genebanks with genotyping by sequencing (GBS). They originated from 26 different countries and represent about 44% of all cauliflower accessions in both genebanks. The analysis of genetic diversity revealed that accessions formed two major groups that represented the two genebanks and were not related to the country of origin. This differentiation was robust with respect to the analysis methods that included principal component analysis, ADMIXTURE and neighbor-joining trees. Genetic diversity was higher in the USDA collection and significant phenotypic differences between the two genebanks were found in three out of six traits investigated. GBS data have a high proportion of missing data, but we observed that the exclusion of single nucleotide polymorphisms (SNPs) with missing data or the imputation of missing SNP alleles produced very similar results. The results indicate that the composition and type of accessions have a strong effect on the structure of genetic diversity of ex situ collections, although regeneration procedures and local adaptation to regeneration conditions may also contribute to a divergence. Fst-based outlier tests of genetic differentiation identified only a small proportion (<1%) of SNPs that are highly differentiated between the two genebanks, which indicates that selection during seed regeneration is not a major cause of differentiation between genebanks. Seed regeneration procedures of both genebanks do not result in different levels of genetic drift and loss of genetic variation. We therefore conclude that the composition and type of accessions mainly influence the level of genetic diversity and explain the strong genetic differentiation between the two ex situ collections. In summary, GBS is a useful method for characterizing genetic diversity in cauliflower genebank material

Identification and expression analysis of cold and freezing stress responsive genes of Brassica oleracea.

PubMed

Ahmed, Nasar Uddin; Jung, Hee-Jeong; Park, Jong-In; Cho, Yong-Gu; Hur, Yoonkang; Nou, Ill-Sup

2015-01-10

Cold and freezing stress is a major environmental constraint to the production of Brassica crops. Enhancement of tolerance by exploiting cold and freezing tolerance related genes offers the most efficient approach to address this problem. Cold-induced transcriptional profiling is a promising approach to the identification of potential genes related to cold and freezing stress tolerance. In this study, 99 highly expressed genes were identified from a whole genome microarray dataset of Brassica rapa. Blast search analysis of the Brassica oleracea database revealed the corresponding homologous genes. To validate their expression, pre-selected cold tolerant and susceptible cabbage lines were analyzed. Out of 99 BoCRGs, 43 were differentially expressed in response to varying degrees of cold and freezing stress in the contrasting cabbage lines. Among the differentially expressed genes, 18 were highly up-regulated in the tolerant lines, which is consistent with their microarray expression. Additionally, 12 BoCRGs were expressed differentially after cold stress treatment in two contrasting cabbage lines, and BoCRG54, 56, 59, 62, 70, 72 and 99 were predicted to be involved in cold regulatory pathways. Taken together, the cold-responsive genes identified in this study provide additional direction for elucidating the regulatory network of low temperature stress tolerance and developing cold and freezing stress resistant Brassica crops. Copyright © 2014 Elsevier B.V. All rights reserved.

BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species.

PubMed

Murukarthick, Jayakodi; Sampath, Perumal; Lee, Sang Choon; Choi, Beom-Soon; Senthil, Natesan; Liu, Shengyi; Yang, Tae-Jin

2014-06-20

MITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops. We have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences. BrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a valuable repository for scientists

Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.

PubMed

Jiang, Jinjin; Wang, Yue; Zhu, Bao; Fang, Tingting; Fang, Yujie; Wang, Youping

2015-01-27

Brassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U's triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale. We examined the gene expression patterns of three diploids (Brassica rapa, B. nigra, and B. oleracea) and three amphidiploids (B. napus, B. juncea, and B. carinata) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in Brassica amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in Brassica species. Our results provided an understanding of the transcriptome complexity of natural Brassica species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among Brassica species.

Complete mitochondrial genome sequences of Brassica rapa (Chinese cabbage and mizuna), and intraspecific differentiation of cytoplasm in B. rapa and Brassica juncea.

PubMed

Hatono, Saki; Nishimura, Kaori; Murakami, Yoko; Tsujimura, Mai; Yamagishi, Hiroshi

2017-09-01

The complete sequence of the mitochondrial genome was determined for two cultivars of Brassica rapa . After determining the sequence of a Chinese cabbage variety, 'Oushou hakusai', the sequence of a mizuna variety, 'Chusei shiroguki sensuji kyomizuna', was mapped against the sequence of Chinese cabbage. The precise sequences where the two varieties demonstrated variation were ascertained by direct sequencing. It was found that the mitochondrial genomes of the two varieties are identical over 219,775 bp, with a single nucleotide polymorphism (SNP) between the genomes. Because B. rapa is the maternal species of an amphidiploid crop species, Brassica juncea , the distribution of the SNP was observed both in B. rapa and B. juncea . While the mizuna type SNP was restricted mainly to cultivars of mizuna (japonica group) in B. rapa , the mizuna type was widely distributed in B. juncea . The finding that the two Brassica species have these SNP types in common suggests that the nucleotide substitution occurred in wild B. rapa before both mitotypes were domesticated. It was further inferred that the interspecific hybridization between B. rapa and B. nigra took place twice and resulted in the two mitotypes of cultivated B. juncea .

Proteomic and comparative genomic analysis reveals adaptability of Brassica napus to phosphorus-deficient stress.

PubMed

Chen, Shuisen; Ding, Guangda; Wang, Zhenhua; Cai, Hongmei; Xu, Fangsen

2015-03-18

Given low solubility and immobility in many soils of the world, phosphorus (P) may be the most widely studied macronutrient for plants. In an attempt to gain an insight into the adaptability of Brassica napus to P deficiency, proteome alterations of roots and leaves in two B. napus contrasting genotypes, P-efficient 'Eyou Changjia' and P-inefficient 'B104-2', under long-term low P stress and short-term P-free starvation conditions were investigated, and proteomic combined with comparative genomic analyses were conducted to interpret the interrelation of differential abundance protein species (DAPs) responding to P deficiency with quantitative trait loci (QTLs) for P deficiency tolerance. P-efficient 'Eyou Changjia' had higher dry weight and P content, and showed high tolerance to low P stress compared with P-inefficient 'B104-2'. A total of 146 DAPs were successfully identified by MALDI TOF/TOF MS, which were categorized into several groups including defense and stress response, carbohydrate and energy metabolism, signaling and regulation, amino acid and fatty acid metabolism, protein process, biogenesis and cellular component, and function unknown. 94 of 146 DAPs were mapped to a linkage map constructed by a B. napus population derived from a cross between the two genotypes, and 72 DAPs were located in the confidence intervals of QTLs for P efficiency related traits. We conclude that the identification of these DAPs and the co-location of DAPs with QTLs in the B. napus linkage genetic map provide us novel information in understanding the adaptability of B. napus to P deficiency, and helpful to isolate P-efficient genes in B. napus. Low P seriously limits the production and quality of B. napus. Proteomics and genetic linkage map were widely used to study the adaptive strategies of B. napus response to P deficiency, proteomic combined with comparative genetic analysis to investigate the correlations between DAPs and QTLs are scarce. Thus, we herein investigated

Improving the biocontrol potential of entomopathogenic nematodes against Mamestra brassicae: effect of spray application technique, adjuvants and an attractant.

PubMed

Beck, Bert; Brusselman, Eva; Nuyttens, David; Moens, Maurice; Temmerman, Femke; Pollet, Sabien; Van Weyenberg, Stephanie; Spanoghe, Pieter

2014-01-01

Steinernema carpocapsae Weiser, an entomopathogenic nematode (EPN), is a potential biological control agent for the cabbage moth (Mamestra brassicae L.). This research aimed to identify a suitable spray application technique, and to determine whether yeast extract added to an EPN spray has an attracting and/or a feeding stimulant effect on M. brassicae. The biological control capabilities of EPN against this pest were examined in the field. Good coverage of the underside of cauliflower leaves, the habitat of young instar larvae (L1-L4) of M. brassicae was obtained using different spray boom configurations with vertical extensions that carried underleaf spraying nozzles. One of the configurations was selected for field testing with an EPN spray. Brewer's yeast extract stimulated larval feeding on leaves, and increased the mortality of these larvae when exposed to EPN. The field trial showed that a spray application with S. carpocapsae, Addit and xanthan gum can effectively lower the numbers of cabbage heads damaged by M. brassicae. Brewer's yeast extract did not significantly increase this field performance of EPN. Steinernema carpocapsae, applied with an appropriate spray technique, can be used within biological control schemes as part of a resistance management programme for Bt. © 2013 Society of Chemical Industry.

Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea

PubMed Central

2013-01-01

Background The Brassica B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacterial artificial chromosome (BAC) library of Brassica nigra was developed and screened with 17 genes from a 222 kb region of A. thaliana that had been well characterised in both the Brassica A and C genomes. Results Fingerprinting of 483 apparently non-redundant clones defined physical contigs for the corresponding regions in B. nigra. The target region is duplicated in A. thaliana and six homologous contigs were found in B. nigra resulting from the whole genome triplication event shared by the Brassiceae tribe. BACs representative of each region were sequenced to elucidate the level of microscale rearrangements across the Brassica species divide. Conclusions Although the B genome species separated from the A/C lineage some 6 Mya, comparisons between the three paleopolyploid Brassica genomes revealed extensive conservation of gene content and sequence identity. The level of fractionation or gene loss varied across genomes and genomic regions; however, the greatest loss of genes was observed to be common to all three genomes. One large-scale chromosomal rearrangement differentiated the B genome suggesting such events could contribute to the lack of recombination observed between B genome species and those of the closely related A/C lineage. PMID:23586706

Distinct subgenome stabilities in synthesized Brassica allohexaploids.

PubMed

Zhou, Jiannan; Tan, Chen; Cui, Cheng; Ge, Xianhong; Li, Zaiyun

2016-07-01

Trigenomic Brassica allohexaploids synthesized from three crossing strategies showed diploidized and non-diploidized meiotic behaviors and produced both euploid and aneuploid progenies during successive generations, revealing the distinct subgenome stabilities (B > A> C). Three cultivated allotetraploid Brassica species (Brassica napus, B. juncea, B. carinata) represent the model system of speciation through interspecific hybridization and allopolyploidization, but no Brassica species at higher ploidy level exists in nature. In this study, Brassica allohexaploids (2n = 54, AABBCC) were artificially synthesized using three crossing strategies, and had combinations of the genomes from the extant allotetraploids and diploids (B. rapa, B. oleracea and B. nigra). The chromosome numbers and complements of these allohexaploids and the self-pollinated progenies of successive generations (S0-S7) were determined using multicolor fluorescent in situ hybridization that distinguished the chromosomes of three constituent genomes from each other. Both euploid and aneuploid progenies were identified. The most aneuploids maintained all B- and A-genome chromosomes and variable number of C-genome chromosomes, suggesting that genome stability was B > A > C. In the extreme case, loss of whole set of C-genome chromosomes led to the production of B. juncea-type progeny. Some aneuploid progenies had the same number of chromosomes (2n = 54) as the euploid, but the simultaneous loss and gain of A- and C-genome chromosomes. The diploidized and non-diploidized meiotic behaviors co-occurred in all allohexaploid individuals of consecutive generations. The aberrant chromosome pairing and segregation mainly involved the chromosomes of A and C genomes, which resulted in aneuploidy in self-pollinated progenies. The mechanisms for the differential stability of three genomes and the stabilization of the new allohexaploids are discussed.

Transgenic increases in seed oil content are associated with the differential expression of novel Brassica-specific transcripts.

PubMed

Sharma, Nirmala; Anderson, Maureen; Kumar, Arvind; Zhang, Yan; Giblin, E Michael; Abrams, Suzanne R; Zaharia, L Irina; Taylor, David C; Fobert, Pierre R

2008-12-19

Seed oil accumulates primarily as triacylglycerol (TAG). While the biochemical pathway for TAG biosynthesis is known, its regulation remains unclear. Previous research identified microsomal diacylglycerol acyltransferase 1 (DGAT1, EC 2.3.1.20) as controlling a rate-limiting step in the TAG biosynthesis pathway. Of note, overexpression of DGAT1 results in substantial increases in oil content and seed size. To further analyze the global consequences of manipulating DGAT1 levels during seed development, a concerted transcriptome and metabolome analysis of transgenic B. napus prototypes was performed. Using a targeted Brassica cDNA microarray, about 200 genes were differentially expressed in two independent transgenic lines analyzed. Interestingly, 24-33% of the targets showing significant changes have no matching gene in Arabidopsis although these represent only 5% of the targets on the microarray. Further analysis of some of these novel transcripts indicated that several are inducible by ABA in microspore-derived embryos. Of the 200 Arabidopsis genes implicated in lipid biology present on the microarray, 36 were found to be differentially regulated in DGAT transgenic lines. Furthermore, kinetic reverse transcriptase Polymerase Chain Reaction (k-PCR) analysis revealed up-regulation of genes encoding enzymes of the Kennedy pathway involved in assembly of TAGs. Hormone profiling indicated that levels of auxins and cytokinins varied between transgenic lines and untransformed controls, while differences in the pool sizes of ABA and catabolites were only observed at later stages of development. Our results indicate that the increased TAG accumulation observed in transgenic DGAT1 plants is associated with modest transcriptional and hormonal changes during seed development that are not limited to the TAG biosynthesis pathway. These might be associated with feedback or feed-forward effects due to altered levels of DGAT1 activity. The fact that a large fraction of significant

Enteric methane production and ruminal fermentation of forage brassica diets fed in continuous culture.

PubMed

Dillard, Sandra Leanne; Roca-Fernández, Ana I; Rubano, Melissa D; Elkin, Kyle R; Soder, Kathy J

2018-04-14

The aim of the current study was to determine nutrient digestibility, VFA production, N metabolism, and CH4 production of canola (Brassica napus L.), rapeseed (B. napus L.), turnip (Brassica rapa L.), and annual ryegrass (Lolium multiflorum Lam.) fed with orchardgrass (Dactylis glomerata L.) in continuous culture. Diets were randomly assigned to fermentors in a 4 × 4 Latin square design using 7 d for adaptation and 3 d for collection. Diets were: 1) 50% orchardgrass + 50% annual ryegrass (ARG); 2) 50% orchardgrass + 50% canola (CAN); 3) 50% orchardgrass + 50% rapeseed (RAP); and 4) 50% orchardgrass + 50% turnip (TUR). Feedings (82 g DM/d) occurred four times daily throughout 4, 10-d periods at 730, 1030, 1400, and 1900 h. Methane samples were collected every 10 min using a photoacoustic gas analyzer (LumaSense Technologies, Inc.; Santa Clara, CA) during the last 3 d of the experiment. Effluent samples were collected on d 8, 9, and 10, composited by fermentor, and analyzed for VFA and pH as well as DM, OM, CP, and fiber fractions for determination of nutrient digestibility. Forage samples were analyzed for CP, NDF, ADF, minerals, and glucosinolate (GLS) concentrations. Data were analyzed using the GLIMMIX procedure of SAS. Apparent DM, OM, and NDF digestibilities and true DM and OM digestibilities were similar (P > 0.28) among diets (45.1, 63.2, 44.1, 67.1, and 87.2%, respectively). Total VFA (87.2 mol/100 mol), pH (6.47), and acetate (A: 44.6 mol/100 mol) were also not different (P > 0.20) among diets. The A:P (P = propionate) ratio was greater (P < 0.01) in ARG and CAN than RAP and TUR. Daily CH4 production was greater (P < 0.01) in ARG than all other diets (68.9 vs. 11.2 mg/d). Methane, whether expressed as g per g of OM, NDF, digestible OM, or digestible NDF fed was greatest (P < 0.01) in ARG but similar (P > 0.18) among brassica diets. A significant negative correlation was observed between total GLS and CH4 production. However, when multiple regression

Metabolic adaptations to short-term every-other-day feeding in long-living Ames dwarf mice.

PubMed

Brown-Borg, Holly M; Rakoczy, Sharlene

2013-09-01

Restrictive dietary interventions exert significant beneficial physiological effects in terms of aging and age-related disease in many species. Every other day feeding (EOD) has been utilized in aging research and shown to mimic many of the positive outcomes consequent with dietary restriction. This study employed long living Ames dwarf mice subjected to EOD feeding to examine the adaptations of the oxidative phosphorylation and antioxidative defense systems to this feeding regimen. Every other day feeding lowered liver glutathione (GSH) concentrations in dwarf and wild type (WT) mice but altered GSH biosynthesis and degradation in WT mice only. The activities of liver OXPHOS enzymes and corresponding proteins declined in WT mice fed EOD while in dwarf animals, the levels were maintained or increased with this feeding regimen. Antioxidative enzymes were differentially affected depending on the tissue, whether proliferative or post-mitotic. Gene expression of components of liver methionine metabolism remained elevated in dwarf mice when compared to WT mice as previously reported however, enzymes responsible for recycling homocysteine to methionine were elevated in both genotypes in response to EOD feeding. The data suggest that the differences in anabolic hormone levels likely affect the sensitivity of long living and control mice to this dietary regimen, with dwarf mice exhibiting fewer responses in comparison to WT mice. These results provide further evidence that dwarf mice may be better protected against metabolic and environmental perturbations which may in turn, contribute to their extended longevity. © 2013.

Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data

PubMed Central

Eckes, Annemarie H.; Gubała, Tomasz; Nowakowski, Piotr; Szymczyszyn, Tomasz; Wells, Rachel; Irwin, Judith A.; Horro, Carlos; Hancock, John M.; King, Graham; Dyer, Sarah C.; Jurkowski, Wiktor

2017-01-01

The Brassica Information Portal (BIP) is a centralised repository for brassica phenotypic data. The site hosts trait data associated with brassica research and breeding experiments conducted on brassica crops, that are used as oilseeds, vegetables, livestock forage and fodder and for biofuels. A key feature is the explicit management of meta-data describing the provenance and relationships between experimental plant materials, as well as trial design and trait descriptors. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for researchers, breeders and other end-users. BIP opens up the opportunity to apply integrative, cross-project analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository. PMID:28529710

Use of a complete starter feed in grain adaptation programs for feedlot cattle.

PubMed

Schneider, C J; Nuttelman, B L; Shreck, A L; Burken, D B; Griffin, W A; Gramkow, J L; Stock, R A; Klopfenstein, T J; Erickson, G E

2017-08-01

Four experiments evaluated the use of a complete starter feed (RAMP; Cargill Corn Milling, Blair, NE) for grain adaptation. In Exp. 1, 229 yearling steers (397 ± 28.4 kg BW) were used to compare a traditional adaptation program (CON) with adapting cattle with RAMP in either a 1- (RAMP-1RS) or 2- (RAMP-2RS) ration system. From d 23 to slaughter, cattle were fed a common finishing diet. In Exp. 2, 390 yearling steers (341 ± 14 kg BW) were used to compare accelerated grain adaptation programs with RAMP with 2 control treatments where RAMP was blended with a finishing diet containing either 25 (CON25) or 47.5% (CON47) Sweet Bran (Cargill Corn Milling) in 4 steps fed over 24 d to adapt cattle. Rapid adaptation treatments involved feeding RAMP for 10 d followed by a blend of RAMP and a 47% Sweet Bran finishing diet to transition cattle with 3 blends fed for 1 d each (3-1d), 2 blends fed for 2 d each (2-2d), or 1 blend fed for 4 d (1-4d). From d 29 to slaughter, all cattle were fed a common finishing diet. In Exp. 3, 300 steer calves (292 ± 21 kg BW) were used to compare the CON47 and 1-4d adaptation programs with directly transitioning cattle from RAMP, which involved feeding RAMP for 10 d and then switching directly to F1 on d 11 (1-STEP). From d 29 until slaughter, F2 was fed to all cattle. In Exp. 4, 7 ruminally fistulated steers (482 ± 49 kg BW) were used in a 35-d trial to compare the CON47 and 1-STEP adaptation programs. Ruminal pH and intake data from the first 6 d of F1and first 6 d of F2 were used to compare adaptation systems. Adaptation with RAMP-1RS and RAMP-2RS increased ( < 0.01) G:F compared with cattle adapted using CON in Exp. 1. Feeding RAMP-1RS increased ADG ( = 0.03) compared with CON. Intakes were similar ( = 0.39) among treatments. Daily gain, DMI, G:F, and carcass traits were similar ( > 0.11) among treatments in Exp. 2. Daily gain, DMI, and G:F were not different ( > 0.20) among treatments on d 39 or over the entire feeding period in Exp. 3

SSR marker variations in Brassica species provide insight into the origin and evolution of Brassica amphidiploids.

PubMed

Thakur, Ajay Kumar; Singh, Kunwar Harendra; Singh, Lal; Nanjundan, Joghee; Khan, Yasin Jeshima; Singh, Dhiraj

2018-01-01

Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U's triangle along with Eruca sativa as an outlier. Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B. juncea and three subspecies of B. rapa , while lowest cross-transferability (91.93%) was obtained for Eruca sativa . The average % age of cross-transferability across all the seven species was 98.15%. The number of alleles detected at each locus ranged from one to six with an average of 3.41 alleles per primer pair. Neighbor-Joining-based dendrogram divided all the 40 accessions into two main groups composed of B. juncea / B. nigra/B. rapa and B. carinata/B. napus/B. oleracea . C-genome of oilseed Brassica species remained relatively more conserved than A- and B-genome. A- genome present in B. juncea and B. napus seems distinct from each other and hence provides great opportunity for generating diversity through synthesizing amphidiploids from different sources of A- genome. B. juncea had least intra-specific distance indicating narrow genetic base. B. rapa appears to be more primitive species from which other two diploid species might have evolved. The SSR marker set developed in this study will assist in DNA fingerprinting of various Brassica species cultivars, evaluating the genetic diversity in Brassica germplasm, genome mapping and construction of linkage maps, gene tagging and various other genomics-related studies in Brassica species. Further, the evolutionary relationship established among various Brassica species would assist in formulating suitable breeding strategies for widening the genetic base of Brassica amphidiploids by exploiting the genetic diversity present in diploid progenitor gene pools.

Feeding guild of non-host community members affects host-foraging efficiency of a parasitic wasp.

PubMed

De Rijk, Marjolein; Yang, Daowei; Engel, Bas; Dicke, Marcel; Poelman, Erik H

2016-06-01

Interactions between predator and prey, or parasitoid and host, are shaped by trait- and density-mediated processes involving other community members. Parasitoids that lay their eggs in herbivorous insects locate their hosts through infochemicals such as herbivore-induced plant volatiles (HIPVs) and host-produced kairomones. Hosts are frequently accompanied by non-host herbivores that are unsuitable for the parasitoid. These non-hosts may interfere with host location primarily through trait-mediated processes, by their own infochemicals, and their induction of the emission of plant volatiles. Although it is known that single non-hosts can interfere with parasitoid host location, it is still unknown whether the observed effects are due to species specific characteristics or to the feeding habits of the non-host herbivores. Here we addressed whether the feeding guild of non-host herbivores differentially affects foraging of the parasitoid Cotesia glomerata for its common host, caterpillars of Pieris brassicae feeding on Brassica oleracea plants. We used different phloem-feeding and leaf-chewing non-hosts to study their effects on host location by the parasitoid when searching for host-infested plants based on HIPVs and when searching for hosts on the plant using infochemicals. To evaluate the ultimate effect of these two phases in host location, we studied parasitism efficiency of parasitoids in small plant communities under field-tent conditions. We show that leaf-chewing non-hosts primarily affected host location through trait-mediated effects via plant volatiles, whereas phloem-feeding non-hosts exerted trait-mediated effects by affecting foraging efficiency of the parasitoid on the plant. These trait-mediated effects resulted in associational susceptibility of hosts in environments with phloem feeders and associational resistance in environments with non-host leaf chewers.

Cranial adaptations for feeding on snails in species of Sibynomorphus (Dipsadidae: Dipsadinae).

PubMed

Dos Santos, Marina Meireles; da Silva, Fernanda Magalhães; Hingst-Zaher, Erika; Machado, Fabio Andrade; Zaher, Hussam El Dine; Prudente, Ana Lúcia da Costa

2017-02-01

Neotropical "goo-eating" dipsadine snakes display a set of morphological and histo-chemical adaptations linked to the capture of their soft-bodied, viscous invertebrate prey. Within this group, species from the genus Sibynomorphus feed chiefly on snails and slugs. Here, we analyzed a series of skull and mandible characters in S. mikanii, S. neuwiedi and S. turgidus using geometric morphometrics, with the aim of assessing morphological adaptations related to slug- and snail-feeding in that genus. We further compared the results with Leptodeira annulata, a species that feeds on vertebrates. To evaluate shape differences of the skull and mandible between species we performed a multivariate analysis of variance and a linear discriminant analysis. Our results show that the narrow, elongate skull in S. mikanii may help with slug ingestion, while asymmetry in teeth number and mandibular shape in S. neuwiedi and S. turgidus are likely related to snail feeding. Copyright © 2016 Elsevier GmbH. All rights reserved.

Characterization of the Mamestra configurata (Lepidoptera: Noctuidae) larval midgut protease complement and adaptation to feeding on artificial diet, Brassica species, and protease inhibitor.

PubMed

Erlandson, Martin A; Hegedus, Dwayne D; Baldwin, Douglas; Noakes, Amy; Toprak, Umut

2010-10-01

The midgut protease profiles from 5th instar Mamestra configurata larvae fed various diets (standard artificial diet, low protein diet, low protein diet with soybean trypsin inhibitor [SBTI], or Brassica napus) were characterized by one-dimensional enzymography in gelatin gels. The gut protease profile of larvae fed B. napus possessed protease activities of molecular masses of approximately 33 and 55 kDa, which were not present in the guts of larvae fed artificial diet. Similarly, larvae fed artificial diet had protease activities of molecular masses of approximately 21, 30, and 100 kDa that were absent in larvae fed B. napus. Protease profiles changed within 12 to 24 h after switching larvae from artificial diet to plant diet and vice versa. The gut protease profiles from larvae fed various other brassicaceous species and lines having different secondary metabolite profiles did not differ despite significant differences in larval growth rates on the different host plants. Genes encoding putative digestive proteolytic enzymes, including four carboxypeptidases, five aminopeptidases, and 48 serine proteases, were identified in cDNA libraries from 4th instar M. configurata midgut tissue. Many of the protease-encoding genes were expressed at similar levels on all diets; however, three chymoptrypsin-like genes (McSP23, McSP27, and McSP37) were expressed at much higher levels on standard artificial diet and diet containing SBTI as was the trypsin-like gene McSP34. The expression of the trypsin-like gene McSP50 was highest on B. napus. The adaptation of M. configurata digestive biochemistry to different diets is discussed in the context of the flexibility of polyphagous insects to changing diet sources.

Segregation for fertility and meiotic stability in novel Brassica allohexaploids.

PubMed

Mwathi, Margaret W; Gupta, Mehak; Atri, Chaya; Banga, Surinder S; Batley, Jacqueline; Mason, Annaliese S

2017-04-01

Allohexaploid Brassica populations reveal ongoing segregation for fertility, while genotype influences fertility and meiotic stability. Creation of a new Brassica allohexaploid species is of interest for the development of a crop type with increased heterosis and adaptability. At present, no naturally occurring, meiotically stable Brassica allohexaploid exists, with little data available on chromosome behaviour and meiotic control in allohexaploid germplasm. In this study, 100 plants from the cross B. carinata × B. rapa (A2 allohexaploid population) and 69 plants from the cross (B. napus × B. carinata) × B. juncea (H2 allohexaploid population) were assessed for fertility and meiotic behaviour. Estimated pollen viability, self-pollinated seed set, number of seeds on the main shoot, number of pods on the main shoot, seeds per ten pods and plant height were measured for both the A2 and H2 populations and for a set of reference control cultivars. The H2 population had high segregation for pollen viability and meiotic stability, while the A2 population was characterised by low pollen fertility and a high level of chromosome loss. Both populations were taller, but had lower average fertility trait values than the control cultivar samples. The study also characterises fertility and meiotic chromosome behaviour in genotypes and progeny sets in heterozygous allotetraploid Brassica derived lines, and indicates that genotypes of the parents and H1 hybrids are affecting chromosome pairing and fertility phenotypes in the H2 population. The identification and characterisation of factors influencing stability in novel allohexaploid Brassica populations will assist in the development of this as a new crop species for food and agricultural benefit.

Forage Brassicas: establishment, management, and challenges

USDA-ARS?s Scientific Manuscript database

Forage Brassicas are annuals that can be utilized as pasture during the spring, summer, and fall grazing seasons. Forage brassicas include varieties of rapeseed (rape), radish, turnip, swede, kale, and hybrids. Brassicas are able to produce up to 4 tons of DM/acre, and varieties of turnip, radish, a...

True and standardized total tract phosphorus digestibility in canola meals from Brassica napus black and Brassica juncea yellow fed to growing pigs.

PubMed

Adhikari, P A; Heo, J M; Nyachoti, C M

2015-01-01

The aim was to determine the true total tract digestibility (TTTD) and standardized total tract digestibility (STTD) of P in canola meals from Brassica napus black (BNB) and Brassica juncea yellow (BJY) fed to growing pigs. Fifty-four barrows with an initial BW of 19.9 ± 0.22 kg (mean ± SEM) were allocated in 3 consecutive blocks to 1 of 9 dietary treatments in a randomized complete block design to give 6 replicate pigs per diet. Dietary treatments were cornstarch based with increasing concentrations of P, that is, 0.8, 1.6, 2.4, and 3.3 g/kg (as-fed basis) from either BNB or BJY as the sole source of P and a gelatin-based P-free diet. Limestone was added to maintain a Ca:total P ratio of 1.2:1 in all diets. All diets contained titanium dioxide (3 g/kg) as an indigestible marker. Daily feed allowance was calculated to supply 2.6 times the maintenance energy requirement based on the BW at the beginning of each period and offered in 2 equal portions at 0800 and 1600 h as a dry mash. Pigs were individually housed in metabolism crates and fed experimental diets for 16 d, including 9 d for adaptation to feed and 5 d for total but separate collection of feces and urine. The apparent total tract digestibility values of P increased from 19.0 to 30.0% for BNB and from 17.3 to 28.3% for BJY as the dietary P content increased from 0.8 to 3.3 g/kg DM. The TTTD of P was determined using the regression analysis as dietary P content increased from 0.8 to 3.3 g/kg whereas the STTD of P was calculated for the diet with the highest P content (i.e., 3.3 g/kg, as-fed basis) using the P-free diet to estimate endogenous P losses (EPL). The total and basal EPL estimates obtained with regression analysis and the P-free diet were 665 ± 0.03 and 209 ± 96 mg/kg DMI, respectively. The TTTD of P was 33.3 and 32.0% in BNB and BJY, respectively. Respective STTD values were 31.0 and 28.3%. The results indicated that the TTTD and STTD of P were comparable in the 2 canola meals from BNB and BJY

Effect of rapid or gradual grain adaptation on subacute acidosis and feed intake by feedlot cattle.

PubMed

Bevans, D W; Beauchemin, K A; Schwartzkopf-Genswein, K S; McKinnon, J J; McAllister, T A

2005-05-01

The effects of grain adaptation protocol on subacute acidosis and feed intake by cattle were studied in a completely randomized experiment using 12 crossbred heifers (384 +/- 25 kg BW). The dietary proportion of concentrate was increased from 40 to 90% (DM basis) either by rapid adaptation (65% concentrate diet fed for 3 d) or by gradual adaptation (five intermediate diets containing 48.3, 56.7, 65.0, 73.3, and 81.7% concentrate, fed for 3 d each). Feed intake and ruminal pH (by indwelling ruminal electrodes) were monitored over 20 d. Mean daily pH variables did not differ (P > or = 0.10) between treatments on any of the 3 or 4 d that 65 or 90% concentrate was fed. Variances of a number of pH variables were greater (P < 0.05) for rapidly adapted heifers than for those on the gradual adaptation protocol during adaptation to 65 and 90% concentrate. Mean hourly pH did not differ over the first 24 h of adaptation to 65% concentrate, but variance of hourly pH tended (P < 0.10) to be greater for rapidly adapted than for gradually adapted heifers for eight of the first 24 h. On the first day of feeding 90% concentrate, ruminal pH tended (P = 0.07) to be less at 11 and 12 h after feeding with rapid adaptation than with gradual adaptation. Variance of hourly pH increased steadily in rapidly adapted heifers from 6 h after feeding onward. Ruminal VFA concentration and osmolality did not differ between treatments. Ruminal lactate concentration was < 1 mM, except in two rapidly adapted heifers and one gradually adapted heifer after introduction to 90% concentrate. Adaptation method did not affect DMI or day-to-day variation in DMI. Detection of acidosis was associated with increased variance in ruminal pH variables. A range of individual responses to grain challenge was observed, but current management strategies for preventing acidosis in pens of cattle are based on responses of the most susceptible individuals. A better understanding of factors governing individual responses

The complete chloroplast genome of two Brassica species, Brassica nigra and B. Oleracea.

PubMed

Seol, Young-Joo; Kim, Kyunghee; Kang, Sang-Ho; Perumal, Sampath; Lee, Jonghoon; Kim, Chang-Kug

2017-03-01

The two Brassica species, Brassica nigra and Brassica oleracea, are important agronomic crops. The chloroplast genome sequences were generated by de novo assembly using whole genome next-generation sequences. The chloroplast genomes of B. nigra and B. oleracea were 153 633 bp and 153 366 bp in size, respectively, and showed conserved typical chloroplast structure. The both chloroplast genomes contained a total of 114 genes including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis revealed that B. oleracea is closely related to B. rapa and B. napus but B. nigra is more diverse than the neighbor species Raphanus sativus.

User Guidelines for the Brassica Database: BRAD.

PubMed

Wang, Xiaobo; Cheng, Feng; Wang, Xiaowu

2016-01-01

The genome sequence of Brassica rapa was first released in 2011. Since then, further Brassica genomes have been sequenced or are undergoing sequencing. It is therefore necessary to develop tools that help users to mine information from genomic data efficiently. This will greatly aid scientific exploration and breeding application, especially for those with low levels of bioinformatic training. Therefore, the Brassica database (BRAD) was built to collect, integrate, illustrate, and visualize Brassica genomic datasets. BRAD provides useful searching and data mining tools, and facilitates the search of gene annotation datasets, syntenic or non-syntenic orthologs, and flanking regions of functional genomic elements. It also includes genome-analysis tools such as BLAST and GBrowse. One of the important aims of BRAD is to build a bridge between Brassica crop genomes with the genome of the model species Arabidopsis thaliana, thus transferring the bulk of A. thaliana gene study information for use with newly sequenced Brassica crops.

Genetic Dissection of Leaf Development in Brassica rapa Using a Genetical Genomics Approach1[W

PubMed Central

Xiao, Dong; Wang, Huange; Basnet, Ram Kumar; Zhao, Jianjun; Lin, Ke; Hou, Xilin; Bonnema, Guusje

2014-01-01

The paleohexaploid crop Brassica rapa harbors an enormous reservoir of morphological variation, encompassing leafy vegetables, vegetable and fodder turnips (Brassica rapa, ssp. campestris), and oil crops, with different crops having very different leaf morphologies. In the triplicated B. rapa genome, many genes have multiple paralogs that may be regulated differentially and contribute to phenotypic variation. Using a genetical genomics approach, phenotypic data from a segregating doubled haploid population derived from a cross between cultivar Yellow sarson (oil type) and cultivar Pak choi (vegetable type) were used to identify loci controlling leaf development. Twenty-five colocalized phenotypic quantitative trait loci (QTLs) contributing to natural variation for leaf morphological traits, leaf number, plant architecture, and flowering time were identified. Genetic analysis showed that four colocalized phenotypic QTLs colocalized with flowering time and leaf trait candidate genes, with their cis-expression QTLs and cis- or trans-expression QTLs for homologs of genes playing a role in leaf development in Arabidopsis (Arabidopsis thaliana). The leaf gene BRASSICA RAPA KIP-RELATED PROTEIN2_A03 colocalized with QTLs for leaf shape and plant height; BRASSICA RAPA ERECTA_A09 colocalized with QTLs for leaf color and leaf shape; BRASSICA RAPA LONGIFOLIA1_A10 colocalized with QTLs for leaf size, leaf color, plant branching, and flowering time; while the major flowering time gene, BRASSICA RAPA FLOWERING LOCUS C_A02, colocalized with QTLs explaining variation in flowering time, plant architectural traits, and leaf size. Colocalization of these QTLs points to pleiotropic regulation of leaf development and plant architectural traits in B. rapa. PMID:24394778

Dynamic Adaptation of Liver Mitochondria to Chronic Alcohol Feeding in Mice

PubMed Central

Han, Derick; Ybanez, Maria D.; Johnson, Heather S.; McDonald, Jeniece N.; Mesropyan, Lusine; Sancheti, Harsh; Martin, Gary; Martin, Alanna; Lim, Atalie M; Dara, Lily; Cadenas, Enrique; Tsukamoto, Hidekazu; Kaplowitz, Neil

2012-01-01

Liver mitochondria undergo dynamic alterations following chronic alcohol feeding to mice. Intragastric alcohol feeding to mice resulted in 1) increased state III respiration (109% compared with control) in isolated liver mitochondria, probably due to increased levels of complexes I, IV, and V being incorporated into the respiratory chain; 2) increased mitochondrial NAD+ and NADH levels (∼2-fold), with no change in the redox status; 3) alteration in mitochondrial morphology, with increased numbers of elongated mitochondria; and 4) enhanced mitochondrial biogenesis in the liver, which corresponded with an up-regulation of PGC-1α (peroxisome proliferator-activated receptor γ coactivator-1α). Oral alcohol feeding to mice, which is associated with less liver injury and steatosis, slightly enhanced respiration in isolated liver mitochondria (30.8% compared with control), lower than the striking increase caused by intragastric alcohol feeding. Mitochondrial respiration increased with both oral and intragastric alcohol feeding despite extensive N-acetylation of mitochondrial proteins. The alcohol-induced mitochondrial alterations are probably an adaptive response to enhance alcohol metabolism in the liver. Isolated liver mitochondria from alcohol-treated mice had a greater rate of acetaldehyde metabolism and respiration when treated with acetaldehyde than control. Aldehyde dehydrogenase-2 levels were unaltered in response to alcohol, suggesting that the greater acetaldehyde metabolism by isolated mitochondria from alcohol-treated mice was due to increased mitochondrial respiration that regenerated NAD+, the rate-limiting substrate in alcohol/acetaldehyde metabolism. Overall, our work suggests that mitochondrial plasticity in the liver may be an important adaptive response to the metabolic stress caused by alcohol intake and could potentially play a role in many other vital functions performed by the liver. PMID:23086958

Field evaluation of leaf blight-resistant plant introductions of Brassica Juncea and Brassica Rapa and elucidation of inheritance of resistance

USDA-ARS?s Scientific Manuscript database

Brassica leafy greens (Brassica juncea and Brassica rapa) represent one of the most economically important vegetable crop groups in the southeastern United States. In the last 10 years, numerous occurrences of a leaf blight disease on these leafy vegetables have been reported in several states. One ...

Sequence and functional characterization of MIRNA164 promoters from Brassica shows copy number dependent regulatory diversification among homeologs.

PubMed

Jain, Aditi; Anand, Saurabh; Singh, Neer K; Das, Sandip

2018-03-12

The impact of polyploidy on functional diversification of cis-regulatory elements is poorly understood. This is primarily on account of lack of well-defined structure of cis-elements and a universal regulatory code. To the best of our knowledge, this is the first report on characterization of sequence and functional diversification of paralogous and homeologous promoter elements associated with MIR164 from Brassica. The availability of whole genome sequence allowed us to identify and isolate a total of 42 homologous copies of MIR164 from diploid species-Brassica rapa (A-genome), Brassica nigra (B-genome), Brassica oleracea (C-genome), and allopolyploids-Brassica juncea (AB-genome), Brassica carinata (BC-genome) and Brassica napus (AC-genome). Additionally, we retrieved homologous sequences based on comparative genomics from Arabidopsis lyrata, Capsella rubella, and Thellungiella halophila, spanning ca. 45 million years of evolutionary history of Brassicaceae. Sequence comparison across Brassicaceae revealed lineage-, karyotype, species-, and sub-genome specific changes providing a snapshot of evolutionary dynamics of miRNA promoters in polyploids. Tree topology of cis-elements associated with MIR164 was found to re-capitulate the species and family evolutionary history. Phylogenetic shadowing identified transcription factor binding sites (TFBS) conserved across Brassicaceae, of which, some are already known as regulators of MIR164 expression. Some of the TFBS were found to be distributed in a sub-genome specific (e.g., SOX specific to promoter of MIR164c from MF2 sub-genome), lineage-specific (YABBY binding motif, specific to C. rubella in MIR164b), or species-specific (e.g., VOZ in A. thaliana MIR164a) manner which might contribute towards genetic and adaptive variation. Reporter activity driven by promoters associated with MIR164 paralogs and homeologs was majorly in agreement with known role of miR164 in leaf shaping, regulation of lateral root development and

Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea.

PubMed

Cheng, Feng; Sun, Rifei; Hou, Xilin; Zheng, Hongkun; Zhang, Fenglan; Zhang, Yangyong; Liu, Bo; Liang, Jianli; Zhuang, Mu; Liu, Yunxia; Liu, Dongyuan; Wang, Xiaobo; Li, Pingxia; Liu, Yumei; Lin, Ke; Bucher, Johan; Zhang, Ningwen; Wang, Yan; Wang, Hui; Deng, Jie; Liao, Yongcui; Wei, Keyun; Zhang, Xueming; Fu, Lixia; Hu, Yunyan; Liu, Jisheng; Cai, Chengcheng; Zhang, Shujiang; Zhang, Shifan; Li, Fei; Zhang, Hui; Zhang, Jifang; Guo, Ning; Liu, Zhiyuan; Liu, Jin; Sun, Chao; Ma, Yuan; Zhang, Haijiao; Cui, Yang; Freeling, Micheal R; Borm, Theo; Bonnema, Guusje; Wu, Jian; Wang, Xiaowu

2016-10-01

Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.

Complete mitochondrial genome sequence of black mustard (Brassica nigra; BB) and comparison with Brassica oleracea (CC) and Brassica carinata (BBCC).

PubMed

Yamagishi, Hiroshi; Tanaka, Yoshiyuki; Terachi, Toru

2014-11-01

Crop species of Brassica (Brassicaceae) consist of three monogenomic species and three amphidiploid species resulting from interspecific hybridizations among them. Until now, mitochondrial genome sequences were available for only five of these species. We sequenced the mitochondrial genome of the sixth species, Brassica nigra (nuclear genome constitution BB), and compared it with those of Brassica oleracea (CC) and Brassica carinata (BBCC). The genome was assembled into a 232 145 bp circular sequence that is slightly larger than that of B. oleracea (219 952 bp). The genome of B. nigra contained 33 protein-coding genes, 3 rRNA genes, and 17 tRNA genes. The cox2-2 gene present in B. oleracea was absent in B. nigra. Although the nucleotide sequences of 52 genes were identical between B. nigra and B. carinata, the second exon of rps3 showed differences including an insertion/deletion (indel) and nucleotide substitutions. A PCR test to detect the indel revealed intraspecific variation in rps3, and in one line of B. nigra it amplified a DNA fragment of the size expected for B. carinata. In addition, the B. carinata lines tested here produced DNA fragments of the size expected for B. nigra. The results indicate that at least two mitotypes of B. nigra were present in the maternal parents of B. carinata.

Quantifying the thermal heat requirement of Brassica in assessing biophysical parameters under semi-arid microenvironments

NASA Astrophysics Data System (ADS)

Adak, Tarun; Chakravarty, N. V. K.

2010-07-01

Evaluation of the thermal heat requirement of Brassica spp. across agro-ecological regions is required in order to understand the further effects of climate change. Spatio-temporal changes in hydrothermal regimes are likely to affect the physiological growth pattern of the crop, which in turn will affect economic yields and crop quality. Such information is helpful in developing crop simulation models to describe the differential thermal regimes that prevail at different phenophases of the crop. Thus, the current lack of quantitative information on the thermal heat requirement of Brassica crops under debranched microenvironments prompted the present study, which set out to examine the response of biophysical parameters [leaf area index (LAI), dry biomass production, seed yield and oil content] to modified microenvironments. Following 2 years of field experiments on Typic Ustocrepts soils under semi-arid climatic conditions, it was concluded that the Brassica crop is significantly responsive to microenvironment modification. A highly significant and curvilinear relationship was observed between LAI and dry biomass production with accumulated heat units, with thermal accumulation explaining ≥80% of the variation in LAI and dry biomass production. It was further observed that the economic seed yield and oil content, which are a function of the prevailing weather conditions, were significantly responsive to the heat units accumulated from sowing to 50% physiological maturity. Linear regression analysis showed that growing degree days (GDD) could indicate 60-70% variation in seed yield and oil content, probably because of the significant response to differential thermal microenvironments. The present study illustrates the statistically strong and significant response of biophysical parameters of Brassica spp. to microenvironment modification in semi-arid regions of northern India.

Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana.

PubMed

Yu, Jingyin; Tehrim, Sadia; Zhang, Fengqi; Tong, Chaobo; Huang, Junyan; Cheng, Xiaohui; Dong, Caihua; Zhou, Yanqiu; Qin, Rui; Hua, Wei; Liu, Shengyi

2014-01-03

Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica oleracea and Brassica rapa provides an important opportunity for researchers to identify and characterize NBS-encoding R genes in Brassica species and to compare with analogues in Arabidopsis thaliana based on a comparative genomics approach. However, little is known about the evolutionary fate of NBS-encoding genes in the Brassica lineage after split from A. thaliana. Here we present genome-wide analysis of NBS-encoding genes in B. oleracea, B. rapa and A. thaliana. Through the employment of HMM search and manual curation, we identified 157, 206 and 167 NBS-encoding genes in B. oleracea, B. rapa and A. thaliana genomes, respectively. Phylogenetic analysis among 3 species classified NBS-encoding genes into 6 subgroups. Tandem duplication and whole genome triplication (WGT) analyses revealed that after WGT of the Brassica ancestor, NBS-encoding homologous gene pairs on triplicated regions in Brassica ancestor were deleted or lost quickly, but NBS-encoding genes in Brassica species experienced species-specific gene amplification by tandem duplication after divergence of B. rapa and B. oleracea. Expression profiling of NBS-encoding orthologous gene pairs indicated the differential expression pattern of retained orthologous gene copies in B. oleracea and B. rapa. Furthermore, evolutionary analysis of CNL type NBS-encoding orthologous gene pairs among 3 species suggested that orthologous genes in B. rapa species have undergone stronger negative selection than those in B .oleracea species. But for TNL type, there are no significant differences in the orthologous gene pairs between the two species. This study is first identification and characterization of NBS-encoding genes in B. rapa and B. oleracea based on whole genome sequences. Through tandem duplication and whole genome

Population differentiation in Pacific salmon: local adaptation, genetic drift, or the environment?

USGS Publications Warehouse

Adkison, Milo D.

1995-01-01

Morphological, behavioral, and life-history differences between Pacific salmon (Oncorhynchus spp.) populations are commonly thought to reflect local adaptation, and it is likewise common to assume that salmon populations separated by small distances are locally adapted. Two alternatives to local adaptation exist: random genetic differentiation owing to genetic drift and founder events, and genetic homogeneity among populations, in which differences reflect differential trait expression in differing environments. Population genetics theory and simulations suggest that both alternatives are possible. With selectively neutral alleles, genetic drift can result in random differentiation despite many strays per generation. Even weak selection can prevent genetic drift in stable populations; however, founder effects can result in random differentiation despite selective pressures. Overlapping generations reduce the potential for random differentiation. Genetic homogeneity can occur despite differences in selective regimes when straying rates are high. In sum, localized differences in selection should not always result in local adaptation. Local adaptation is favored when population sizes are large and stable, selection is consistent over large areas, selective diffeentials are large, and straying rates are neither too high nor too low. Consideration of alternatives to local adaptation would improve both biological research and salmon conservation efforts.

Expression of leaf blight resistance in Brassica leafy greens under field conditions and inheritance of resistance in a Brassica juncea source

USDA-ARS?s Scientific Manuscript database

Brassica leafy greens are one of the most economically important vegetable commodities grown in the southeastern United States, and more than 28,000 metric tons of these crops are harvested in the U.S. annually. Collards and kale (Brassica oleracea L.), mustard greens (Brassica juncea L.) and turni...

Comparative Transcriptome Analyses Reveal a Special Glucosinolate Metabolism Mechanism in Brassica alboglabra Sprouts

PubMed Central

Guo, Rongfang; Huang, Zhongkai; Deng, Yanping; Chen, Xiaodong; XuHan, Xu; Lai, Zhongxiong

2016-01-01

Brassica sprouts contain abundant phytochemicals, especially glucosinolates (GSs). Various methods have been used to enhance GS content in sprouts. However, the molecular basis of GS metabolism in sprouts remains an open question. Here we employed RNA-seq analysis to compare the transcriptomes of high-GS (JL-08) and low-GS (JL-09) Brassica alboglabra sprouts. Paired-end Illumina RNA-seq reads were generated and mapped to the Brassica oleracea reference genome. The differentially expressed genes were analyzed between JL-08 and JL-09. Among these, 1477 genes were up-regulated and 1239 down-regulated in JL-09 compared with JL-08. Enrichment analysis of these differentially expressed genes showed that the GS biosynthesis had the smallest enrichment factor and the highest Q-value of all metabolic pathways in Kyoto Encyclopedia of Genes and Genomes database, indicating the main metabolic difference between JL-08 and JL-09 is the GS biosynthetic pathway. Thirty-seven genes of the sequenced data were annotated as putatively involved in GS biosynthesis, degradation, and regulation, of which 11 were differentially expressed in JL-08 and JL-09. The expression level of GS degradation enzyme myrosinase in high-GS JL-08 was lower compared with low-GS JL-09. Surprisingly, in high-GS JL-08, the expression levels of GS biosynthesis genes were also lower than those in low-GS JL-09. As the GS contents in sprouts are determined by dynamic equilibrium of seed stored GS mobilization, de novo synthesis, degradation, and extra transport, the result of this study leads us to suggest that efforts to increase GS content should focus on either raising GS content in seeds or decreasing myrosinase activity, rather than improving the expression level of GS biosynthesis genes in sprouts. PMID:27757119

Gene Silencing of BnTT10 Family Genes Causes Retarded Pigmentation and Lignin Reduction in the Seed Coat of Brassica napus

PubMed Central

Zhang, Kai; Lu, Kun; Qu, Cunmin; Liang, Ying; Wang, Rui; Chai, Yourong; Li, Jiana

2013-01-01

Yellow-seed (i.e., yellow seed coat) is one of the most important agronomic traits of Brassica plants, which is correlated with seed oil and meal qualities. Previous studies on the Brassicaceae, including Arabidopsis and Brassica species, proposed that the seed-color trait is correlative to flavonoid and lignin biosynthesis, at the molecular level. In Arabidopsis thaliana, the oxidative polymerization of flavonoid and biosynthesis of lignin has been demonstrated to be catalyzed by laccase 15, a functional enzyme encoded by the AtTT10 gene. In this study, eight Brassica TT10 genes (three from B. napus, three from B. rapa and two from B. oleracea) were isolated and their roles in flavonoid oxidation/polymerization and lignin biosynthesis were investigated. Based on our phylogenetic analysis, these genes could be divided into two groups with obvious structural and functional differentiation. Expression studies showed that Brassica TT10 genes are active in developing seeds, but with differential expression patterns in yellow- and black-seeded near-isogenic lines. For functional analyses, three black-seeded B. napus cultivars were chosen for transgenic studies. Transgenic B. napus plants expressing antisense TT10 constructs exhibited retarded pigmentation in the seed coat. Chemical composition analysis revealed increased levels of soluble proanthocyanidins, and decreased extractable lignin in the seed coats of these transgenic plants compared with that of the controls. These findings indicate a role for the Brassica TT10 genes in proanthocyanidin polymerization and lignin biosynthesis, as well as seed coat pigmentation in B. napus. PMID:23613820

Genome Wide Identification and Expression Profiling of SWEET Genes Family Reveals Its Role During Plasmodiophora brassicae-Induced Formation of Clubroot in Brassica rapa.

PubMed

Li, Hong; Li, Xiaonan; Xuan, Yuanhu; Jiang, Jing; Wei, Yangdou; Piao, Zhongyun

2018-01-01

Plasmodiophora brassicae is a soil borne pathogen and the causal agent of clubroot, a devastating disease of Brassica crops. The pathogen lives inside roots, and hijacks nutrients from the host plants. It is suggested that clubroot galls created an additional nutrient sink in infected roots. However, the molecular mechanism underlying P. brassicae infection and sugar transport is unclear. Here, we analyzed sugar contents in leaves and roots before and after P. brassicae infection using a pair of Chinese cabbage near-isogenic lines (NILs), carrying either a clubroot resistant (CR) or susceptible (CS) allele at the CRb locus. P. brassicae infection caused significant increase of glucose and fructose contents in the root of CS-NIL compared to CR-NIL, suggesting that sugar translocation and P. brassicae growth are closely related. Among 32 B. rapa SWEET homologs, several BrSWEETs belonging to Clade I and III were significantly up-regulated, especially in CS-NIL upon P. brassicae infection. Moreover, Arabidopsis sweet11 mutant exhibited slower gall formation compared to the wild-type plants. Our studies suggest that P. brassicae infection probably triggers active sugar translocation between the sugar producing tissues and the clubbed tissues, and the SWEET family genes are involved in this process.

Comparative Transcriptome Analysis between Broccoli (Brassica oleracea var. italica) and Wild Cabbage (Brassica macrocarpa Guss.) in Response to Plasmodiophora brassicae during Different Infection Stages.

PubMed

Zhang, Xiaoli; Liu, Yumei; Fang, Zhiyuan; Li, Zhansheng; Yang, Limei; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao

2016-01-01

Clubroot, one of the most devastating diseases to the Brassicaceae family, is caused by the obligate biotrophic pathogen Plasmodiophora brassicae . However, studies of the molecular basis of disease resistance are still poor especially in quantitative resistance. In the present paper, two previously identified genotypes, a clubroot-resistant genotype (wild cabbage, B2013) and a clubroot-susceptible genotype (broccoli, 90196) were inoculated by P. brassicae for 0 (T0), 7 (T7), and 14 (T14) day after inoculation (DAI). Gene expression pattern analysis suggested that response changes in transcript level of two genotypes under P. brassicae infection were mainly activated at the primary stage (T7). Based on the results of DEGs functional enrichments from two infection stages, genes associated with cell wall biosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction showed down-regulated at T14 compared to T7, indicating that defense responses to P. brassicae were induced earlier, and related pathways were repressed at T14. In addition, the genes related to NBS-LRR proteins, SA signal transduction, cell wall and phytoalexins biosynthesis, chitinase, Ca 2+ signals and RBOH proteins were mainly up-regulated in B2013 by comparing those of 90196, indicating the pathways of response defense to clubroot were activated in the resistant genotype. This is the first report about comparative transcriptome analysis for broccoli and its wild relative during the different stages of P. brassicae infection and the results should be useful for molecular assisted screening and breeding of clubroot-resistant genotypes.

Comparative Transcriptome Analysis between Broccoli (Brassica oleracea var. italica) and Wild Cabbage (Brassica macrocarpa Guss.) in Response to Plasmodiophora brassicae during Different Infection Stages

PubMed Central

Zhang, Xiaoli; Liu, Yumei; Fang, Zhiyuan; Li, Zhansheng; Yang, Limei; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao

2016-01-01

Clubroot, one of the most devastating diseases to the Brassicaceae family, is caused by the obligate biotrophic pathogen Plasmodiophora brassicae. However, studies of the molecular basis of disease resistance are still poor especially in quantitative resistance. In the present paper, two previously identified genotypes, a clubroot-resistant genotype (wild cabbage, B2013) and a clubroot-susceptible genotype (broccoli, 90196) were inoculated by P. brassicae for 0 (T0), 7 (T7), and 14 (T14) day after inoculation (DAI). Gene expression pattern analysis suggested that response changes in transcript level of two genotypes under P. brassicae infection were mainly activated at the primary stage (T7). Based on the results of DEGs functional enrichments from two infection stages, genes associated with cell wall biosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction showed down-regulated at T14 compared to T7, indicating that defense responses to P. brassicae were induced earlier, and related pathways were repressed at T14. In addition, the genes related to NBS-LRR proteins, SA signal transduction, cell wall and phytoalexins biosynthesis, chitinase, Ca2+ signals and RBOH proteins were mainly up-regulated in B2013 by comparing those of 90196, indicating the pathways of response defense to clubroot were activated in the resistant genotype. This is the first report about comparative transcriptome analysis for broccoli and its wild relative during the different stages of P. brassicae infection and the results should be useful for molecular assisted screening and breeding of clubroot-resistant genotypes. PMID:28066482

Evaluating relative contribution of osmotolerance and tissue tolerance mechanisms toward salinity stress tolerance in three Brassica species.

PubMed

Chakraborty, Koushik; Bose, Jayakumar; Shabala, Lana; Eyles, Alieta; Shabala, Sergey

2016-10-01

Three different species of Brassica, with differential salt sensitivity were used to understand physiological mechanisms of salt tolerance operating in these species and to evaluate the relative contribution of different strategies to cope with salt load. Brassica napus was the most tolerant species in terms of the overall performance, with Brassica juncea and Brassica oleracea being much more sensitive to salt stress with no obvious difference between them. While prominent reduction in net CO2 assimilation was observed in both sensitive species, physiological mechanisms beyond this reduction differed strongly. Brassica juncea plants possessed high osmotolerance and were able to maintain high transpiration rate but showed a significant reduction in leaf chlorophyll content and efficiency of leaf photochemistry. On the contrary, B. oleracea plants possessed the highest (among the three species) tissue tolerance but showed a very significant stomatal limitation of photosynthesis. Electrophysiological experiments revealed that the high tissue tolerance in B. oleracea was related to the ability of leaf mesophyll cells to maintain highly negative membrane potential in the presence of high apoplastic Na(+) . In addition to high osmotolerance, the most tolerant B. napus showed also lesser accumulation of toxic Na(+) and Cl(-) in the leaf, possessed moderate tissue tolerance and had a superior K(+) retention ability. Taken together, the results from this study indicate that the three Brassica species employ very different mechanisms to cope with salinity and, despite its overall sensitivity to salinity, B. oleracea could be recommended as a valuable 'donor' of tissue tolerance genes to confer this trait for marker-assisted breeding programs. © 2016 Scandinavian Plant Physiology Society.

Differential effect of visual motion adaption upon visual cortical excitability.

PubMed

Lubeck, Astrid J A; Van Ombergen, Angelique; Ahmad, Hena; Bos, Jelte E; Wuyts, Floris L; Bronstein, Adolfo M; Arshad, Qadeer

2017-03-01

The objectives of this study were 1 ) to probe the effects of visual motion adaptation on early visual and V5/MT cortical excitability and 2 ) to investigate whether changes in cortical excitability following visual motion adaptation are related to the degree of visual dependency, i.e., an overreliance on visual cues compared with vestibular or proprioceptive cues. Participants were exposed to a roll motion visual stimulus before, during, and after visual motion adaptation. At these stages, 20 transcranial magnetic stimulation (TMS) pulses at phosphene threshold values were applied over early visual and V5/MT cortical areas from which the probability of eliciting a phosphene was calculated. Before and after adaptation, participants aligned the subjective visual vertical in front of the roll motion stimulus as a marker of visual dependency. During adaptation, early visual cortex excitability decreased whereas V5/MT excitability increased. After adaptation, both early visual and V5/MT excitability were increased. The roll motion-induced tilt of the subjective visual vertical (visual dependence) was not influenced by visual motion adaptation and did not correlate with phosphene threshold or visual cortex excitability. We conclude that early visual and V5/MT cortical excitability is differentially affected by visual motion adaptation. Furthermore, excitability in the early or late visual cortex is not associated with an increase in visual reliance during spatial orientation. Our findings complement earlier studies that have probed visual cortical excitability following motion adaptation and highlight the differential role of the early visual cortex and V5/MT in visual motion processing. NEW & NOTEWORTHY We examined the influence of visual motion adaptation on visual cortex excitability and found a differential effect in V1/V2 compared with V5/MT. Changes in visual excitability following motion adaptation were not related to the degree of an individual's visual

High-throughput multiplex cpDNA resequencing clarifies the genetic diversity and genetic relationships among Brassica napus, Brassica rapa and Brassica oleracea.

PubMed

Qiao, Jiangwei; Cai, Mengxian; Yan, Guixin; Wang, Nian; Li, Feng; Chen, Binyun; Gao, Guizhen; Xu, Kun; Li, Jun; Wu, Xiaoming

2016-01-01

Brassica napus (rapeseed) is a recent allotetraploid plant and the second most important oilseed crop worldwide. The origin of B. napus and the genetic relationships with its diploid ancestor species remain largely unresolved. Here, chloroplast DNA (cpDNA) from 488 B. napus accessions of global origin, 139 B. rapa accessions and 49 B. oleracea accessions were populationally resequenced using Illumina Solexa sequencing technologies. The intraspecific cpDNA variants and their allelic frequencies were called genomewide and further validated via EcoTILLING analyses of the rpo region. The cpDNA of the current global B. napus population comprises more than 400 variants (SNPs and short InDels) and maintains one predominant haplotype (Bncp1). Whole-genome resequencing of the cpDNA of Bncp1 haplotype eliminated its direct inheritance from any accession of the B. rapa or B. oleracea species. The distribution of the polymorphism information content (PIC) values for each variant demonstrated that B. napus has much lower cpDNA diversity than B. rapa; however, a vast majority of the wild and cultivated B. oleracea specimens appeared to share one same distinct cpDNA haplotype, in contrast to its wild C-genome relatives. This finding suggests that the cpDNA of the three Brassica species is well differentiated. The predominant B. napus cpDNA haplotype may have originated from uninvestigated relatives or from interactions between cpDNA mutations and natural/artificial selection during speciation and evolution. These exhaustive data on variation in cpDNA would provide fundamental data for research on cpDNA and chloroplasts. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Quantitative proteomics reveals the importance of nitrogen source to control glucosinolate metabolism in Arabidopsis thaliana and Brassica oleracea

PubMed Central

Marino, Daniel; Ariz, Idoia; Lasa, Berta; Santamaría, Enrique; Fernández-Irigoyen, Joaquín; González-Murua, Carmen; Aparicio Tejo, Pedro M.

2016-01-01

Accessing different nitrogen (N) sources involves a profound adaptation of plant metabolism. In this study, a quantitative proteomic approach was used to further understand how the model plant Arabidopsis thaliana adjusts to different N sources when grown exclusively under nitrate or ammonium nutrition. Proteome data evidenced that glucosinolate metabolism was differentially regulated by the N source and that both TGG1 and TGG2 myrosinases were more abundant under ammonium nutrition, which is generally considered to be a stressful situation. Moreover, Arabidopsis plants displayed glucosinolate accumulation and induced myrosinase activity under ammonium nutrition. Interestingly, these results were also confirmed in the economically important crop broccoli (Brassica oleracea var. italica). Moreover, these metabolic changes were correlated in Arabidopsis with the differential expression of genes from the aliphatic glucosinolate metabolic pathway. This study underlines the importance of nitrogen nutrition and the potential of using ammonium as the N source in order to stimulate glucosinolate metabolism, which may have important applications not only in terms of reducing pesticide use, but also for increasing plants’ nutritional value. PMID:27085186

Comparative morphology of the mouthparts of the megadiverse South African monkey beetles (Scarabaeidae: Hopliini): feeding adaptations and guild structure

PubMed Central

Hansal, Teresa; Krenn, Harald W.; Colville, Jonathan F.

2016-01-01

Although anthophilous Coleoptera are regarded to be unspecialised flower-visiting insects, monkey beetles (Scarabaeidae: Hopliini) represent one of the most important groups of pollinating insects in South Africa’s floristic hotspot of the Greater Cape Region. South African monkey beetles are known to feed on floral tissue; however, some species seem to specialise on pollen and/or nectar. The present study examined the mouthpart morphology and gut content of various hopliine species to draw conclusions on their feeding preferences. According to the specialisations of their mouthparts, the investigated species were classified into different feeding groups. Adaptations to pollen-feeding included a well-developed, toothed molar and a lobe-like, setose lacinia mobilis on the mandible as well as curled hairs or sclerotized teeth on the galea of the maxillae. Furthermore, elongated mouthparts were interpreted as adaptations for nectar feeding. Floral- and folial-tissue feeding species showed sclerotized teeth on the maxilla, but the lacinia was mostly found to be reduced to a sclerotized ledge. While species could clearly be identified as floral or folial tissue feeding, several species showed intermediate traits suggesting both pollen and nectar feeding adaptations. Mismatches found between mouthpart morphology and previously reported flower visiting behaviours across different genera and species requires alternative explanations, not necessarily associated with feeding preferences. Although detailed examinations of the mouthparts allowed conclusions about the feeding preference and flower-visiting behaviour, additional morphological and behavioural investigations, combined with greater taxon sampling and phylogenetic data, are still necessary to fully understand hopliine host plant relationships, related to monkey beetle diversity. PMID:26819850

BRAD, the genetics and genomics database for Brassica plants.

PubMed

Cheng, Feng; Liu, Shengyi; Wu, Jian; Fang, Lu; Sun, Silong; Liu, Bo; Li, Pingxia; Hua, Wei; Wang, Xiaowu

2011-10-13

Brassica species include both vegetable and oilseed crops, which are very important to the daily life of common human beings. Meanwhile, the Brassica species represent an excellent system for studying numerous aspects of plant biology, specifically for the analysis of genome evolution following polyploidy, so it is also very important for scientific research. Now, the genome of Brassica rapa has already been assembled, it is the time to do deep mining of the genome data. BRAD, the Brassica database, is a web-based resource focusing on genome scale genetic and genomic data for important Brassica crops. BRAD was built based on the first whole genome sequence and on further data analysis of the Brassica A genome species, Brassica rapa (Chiifu-401-42). It provides datasets, such as the complete genome sequence of B. rapa, which was de novo assembled from Illumina GA II short reads and from BAC clone sequences, predicted genes and associated annotations, non coding RNAs, transposable elements (TE), B. rapa genes' orthologous to those in A. thaliana, as well as genetic markers and linkage maps. BRAD offers useful searching and data mining tools, including search across annotation datasets, search for syntenic or non-syntenic orthologs, and to search the flanking regions of a certain target, as well as the tools of BLAST and Gbrowse. BRAD allows users to enter almost any kind of information, such as a B. rapa or A. thaliana gene ID, physical position or genetic marker. BRAD, a new database which focuses on the genetics and genomics of the Brassica plants has been developed, it aims at helping scientists and breeders to fully and efficiently use the information of genome data of Brassica plants. BRAD will be continuously updated and can be accessed through http://brassicadb.org.

Insecticidal activity of bio-oil from the pyrolysis of straw from Brassica spp.

PubMed

Suqi, Liu; Cáceres, Luis A; Caceres, Luis; Schieck, Katie; McGarvey, Brian D; Booker, Christina J; McGarvey, Brian M; Yeung, Ken K-C; Pariente, Stephane; Briens, Cedric; Berruti, Franco; Scott, Ian M

2014-04-23

Agricultural crop residues can be converted through thermochemical pyrolysis to bio-oil, a sustainable source of biofuel and biochemicals. The pyrolysis bio-oil is known to contain many chemicals, some of which have insecticidal activity and can be a potential source of value-added pest control products. Brassicacae crops, cabbage, broccoli, and mustards, contain glucosinolates and isocyanates, compounds with recognized anti-herbivore activity. In Canada, canola Brassica napus straw is available from over 6 000 000 ha and mustard Brassica carinata and Brassica juncea straw is available from 200 000 ha. The straw can be converted by microbial lignocellulosic enzymes as a substrate for bioethanol production but can also be converted to bio-oil by thermochemical means. Straw from all three species was pyrolyzed, and the insecticidal components in the bio-oil were isolated by bioassay-guided solvent fractionation. Of particular interest were the mustard straw bio-oil aqueous fractions with insecticidal and feeding repellent activity to Colorado potato beetle larvae. Aqueous fractions further analyzed for active compounds were found not to contain many of the undesirable phenol compounds, which were previously found in other bio-oils seen in the dichloromethane (DCM) and ethyl acetate (EA) solvent phases of the present study. Identified within the most polar fractions were hexadecanoic and octadecanoic fatty acids, indicating that separation of these compounds during bio-oil production may provide a source of effective insecticidal compounds.

Human adaptation and population differentiation in the light of ancient genomes

PubMed Central

Key, Felix M.; Fu, Qiaomei; Romagné, Frédéric; Lachmann, Michael; Andrés, Aida M.

2016-01-01

The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation. PMID:26988143

Identifying Differential Item Functioning in Multi-Stage Computer Adaptive Testing

ERIC Educational Resources Information Center

Gierl, Mark J.; Lai, Hollis; Li, Johnson

2013-01-01

The purpose of this study is to evaluate the performance of CATSIB (Computer Adaptive Testing-Simultaneous Item Bias Test) for detecting differential item functioning (DIF) when items in the matching and studied subtest are administered adaptively in the context of a realistic multi-stage adaptive test (MST). MST was simulated using a 4-item…

Fetal over- and undernutrition differentially program thyroid axis adaptability in adult sheep.

PubMed

Johnsen, L; Lyckegaard, N B; Khanal, P; Quistorff, B; Raun, K; Nielsen, M O

2018-05-01

We aimed to test, whether fetal under- or overnutrition differentially program the thyroid axis with lasting effects on energy metabolism, and if early-life postnatal overnutrition modulates implications of prenatal programming. Twin-pregnant sheep ( n  = 36) were either adequately (NORM), under- (LOW; 50% of NORM) or overnourished (HIGH; 150% of energy and 110% of protein requirements) in the last-trimester of gestation. From 3 days-of-age to 6 months-of-age, twin lambs received a conventional (CONV) or an obesogenic, high-carbohydrate high-fat (HCHF) diet. Subgroups were slaughtered at 6-months-of-age. Remaining lambs were fed a low-fat diet until 2½ years-of-age (adulthood). Serum hormone levels were determined at 6 months- and 2½ years-of-age. At 2½ years-of-age, feed intake capacity (intake over 4-h following 72-h fasting) was determined, and an intravenous thyroxine tolerance test (iTTT) was performed, including measurements of heart rate, rectal temperature and energy expenditure (EE). In the iTTT, the LOW and nutritionally mismatched NORM:HCHF and HIGH:CONV sheep increased serum T 3 , T 3 :T 4 and T 3 :TSH less than NORM:CONV, whereas TSH was decreased less in HIGH, NORM:HCHF and LOW:HCHF. Early postnatal exposure to the HCHF diet decreased basal adult EE in NORM and HIGH, but not LOW, and increased adult feed intake capacity in NORM and LOW, but not HIGH. Conclusions : The iTTT revealed a differential programming of central and peripheral HPT axis function in response to late fetal malnutrition and an early postnatal obesogenic diet, with long-term implications for adult HPT axis adaptability and associated consequences for adiposity risk. © 2018 The authors.

Fetal over- and undernutrition differentially program thyroid axis adaptability in adult sheep

PubMed Central

Johnsen, L; Lyckegaard, N B; Khanal, P; Quistorff, B; Raun, K; Nielsen, M O

2018-01-01

Objective We aimed to test, whether fetal under- or overnutrition differentially program the thyroid axis with lasting effects on energy metabolism, and if early-life postnatal overnutrition modulates implications of prenatal programming. Design Twin-pregnant sheep (n = 36) were either adequately (NORM), under- (LOW; 50% of NORM) or overnourished (HIGH; 150% of energy and 110% of protein requirements) in the last-trimester of gestation. From 3 days-of-age to 6 months-of-age, twin lambs received a conventional (CONV) or an obesogenic, high-carbohydrate high-fat (HCHF) diet. Subgroups were slaughtered at 6-months-of-age. Remaining lambs were fed a low-fat diet until 2½ years-of-age (adulthood). Methods Serum hormone levels were determined at 6 months- and 2½ years-of-age. At 2½ years-of-age, feed intake capacity (intake over 4-h following 72-h fasting) was determined, and an intravenous thyroxine tolerance test (iTTT) was performed, including measurements of heart rate, rectal temperature and energy expenditure (EE). Results In the iTTT, the LOW and nutritionally mismatched NORM:HCHF and HIGH:CONV sheep increased serum T3, T3:T4 and T3:TSH less than NORM:CONV, whereas TSH was decreased less in HIGH, NORM:HCHF and LOW:HCHF. Early postnatal exposure to the HCHF diet decreased basal adult EE in NORM and HIGH, but not LOW, and increased adult feed intake capacity in NORM and LOW, but not HIGH. Conclusions: The iTTT revealed a differential programming of central and peripheral HPT axis function in response to late fetal malnutrition and an early postnatal obesogenic diet, with long-term implications for adult HPT axis adaptability and associated consequences for adiposity risk. PMID:29794141

Adolescents' perception of parental feeding practices: Adaptation and validation of the Comprehensive Feeding Practices Questionnaire for Brazilian adolescents—The CFPQ-Teen

PubMed Central

Piccoli, Ângela Bein; Neiva-Silva, Lucas; Mosmann, Clarisse Pereira; Musher-Eizenman, Dara; Pellanda, Lucia C.

2017-01-01

Background Parental feeding practices may play a key role in dietary habits and nutritional status of adolescents, but research from adolescents’ point of view on this topic is scarce. Objective To adapt and validate an instrument of parental feeding practices as perceived by adolescents in a Brazilian setting. Methods The Comprehensive Feeding Practices Questionnaire was translated into Portuguese and adapted to be answered by adolescents (ages 12 to 18). Content analysis and FACE validity to assess cultural equivalence was undertaken by experts in the adolescent nutritional and psychological fields. Pilot study was evaluated in 23 adolescents. The final version was administered to 41 students to assess instrument reproducibility (Intraclass Correlation Coefficient). Internal consistency (Cronbach's Alpha) and construct validity (Confirmatory Factor Analysis) were assessed in a third sample of 307 adolescents. Results Experts and adolescents considered content validity as appropriate. In reproducibility analysis (Intraclass Correlation Coefficient), 10 of the 12 factors were above 0.7. The factors “teaching about nutrition” and “food as reward” obtained values of 0.60 and 0.68, respectively. The Cronbach's Alpha of the whole scale was 0.83 and alphas for subscales ranged from 0.52 to 0.85; the factors “teaching about nutrition” and “food as a reward” had the lowest values (0.52). After removing these two factors, the Confirmatory Factor Analysis indicated that the structural model was appropriate. The final scale was made up of 10 factors with 43 questions. Conclusions The Comprehensive Feeding Practices Questionnaire-Teen demonstrates validity and reliability, and is a suitable tool to evaluate the perceptions of adolescents regarding parental feeding practices. PMID:29145485

Genome-wide identification of aquaporin encoding genes in Brassica oleracea and their phylogenetic sequence comparison to Brassica crops and Arabidopsis

PubMed Central

Diehn, Till A.; Pommerrenig, Benjamin; Bernhardt, Nadine; Hartmann, Anja; Bienert, Gerd P.

2015-01-01

Aquaporins (AQPs) are essential channel proteins that regulate plant water homeostasis and the uptake and distribution of uncharged solutes such as metalloids, urea, ammonia, and carbon dioxide. Despite their importance as crop plants, little is known about AQP gene and protein function in cabbage (Brassica oleracea) and other Brassica species. The recent releases of the genome sequences of B. oleracea and Brassica rapa allow comparative genomic studies in these species to investigate the evolution and features of Brassica genes and proteins. In this study, we identified all AQP genes in B. oleracea by a genome-wide survey. In total, 67 genes of four plant AQP subfamilies were identified. Their full-length gene sequences and locations on chromosomes and scaffolds were manually curated. The identification of six additional full-length AQP sequences in the B. rapa genome added to the recently published AQP protein family of this species. A phylogenetic analysis of AQPs of Arabidopsis thaliana, B. oleracea, B. rapa allowed us to follow AQP evolution in closely related species and to systematically classify and (re-) name these isoforms. Thirty-three groups of AQP-orthologous genes were identified between B. oleracea and Arabidopsis and their expression was analyzed in different organs. The two selectivity filters, gene structure and coding sequences were highly conserved within each AQP subfamily while sequence variations in some introns and untranslated regions were frequent. These data suggest a similar substrate selectivity and function of Brassica AQPs compared to Arabidopsis orthologs. The comparative analyses of all AQP subfamilies in three Brassicaceae species give initial insights into AQP evolution in these taxa. Based on the genome-wide AQP identification in B. oleracea and the sequence analysis and reprocessing of Brassica AQP information, our dataset provides a sequence resource for further investigations of the physiological and molecular functions of

Differential Costs of Two Distinct Resistance Mechanisms Induced by Different Herbivore Species in Arabidopsis1

PubMed Central

Reichelt, Michael; van Doorn, Arjen; Schuurink, Robert C.

2016-01-01

Plants respond to herbivory with the induction of resistance, mediated by distinct phytohormonal signaling pathways and their interactions. Phloem feeders are known to induce plant resistance via the salicylic acid pathway, whereas biting-chewing herbivores induce plant resistance mainly via the jasmonate pathway. Here, we show that a specialist caterpillar (biting-chewing herbivore) and a specialist aphid (phloem feeder) differentially induce resistance against Pieris brassicae caterpillars in Arabidopsis (Arabidopsis thaliana) plants. Caterpillar feeding induces resistance through the jasmonate signaling pathway that is associated with the induction of kaempferol 3,7-dirhamnoside, whereas aphid feeding induces resistance via a novel mechanism involving sinapoyl malate. The role of sinapoyl malate is confirmed through the use of a mutant compromised in the biosynthesis of this compound. Caterpillar-induced resistance is associated with a lower cost in terms of plant growth reduction than aphid-induced resistance. A strong constitutive resistance against P. brassicae caterpillars in combination with a strong growth attenuation in plants of a transfer DNA (T-DNA) insertion mutant of WRKY70 (wrky70) suggest that the WRKY70 transcription factor, a regulator of downstream responses mediated by jasmonate-salicylic acid signaling cross talk, is involved in the negative regulation of caterpillar resistance and in the tradeoff between growth and defense. In conclusion, different mechanisms of herbivore-induced resistance come with different costs, and a functional WRKY70 transcription factor is required for the induction of low-cost resistance. PMID:26603653

The Gastropod Menace: Slugs on Brassica Plants Affect Caterpillar Survival through Consumption and Interference with Parasitoid Attraction.

PubMed

Desurmont, Gaylord A; Zemanova, Miriam A; Turlings, Ted C J

2016-03-01

Terrestrial molluscs and insect herbivores play a major role as plant consumers in a number of ecosystems, but their direct and indirect interactions have hardly been explored. The omnivorous nature of slugs makes them potential disrupters of predator-prey relationships, as a direct threat to small insects and through indirect, plant-mediated effects. Here, we examined the effects of the presence of two species of slugs, Arion rufus (native) and A. vulgaris (invasive) on the survivorship of young Pieris brassicae caterpillars when feeding on Brassica rapa plants, and on plant attractiveness to the main natural enemy of P. brassicae, the parasitoid Cotesia glomerata. In two separate predation experiments, caterpillar mortality was significantly higher on plants co-infested with A. rufus or A. vulgaris. Moreover, caterpillar mortality correlated positively with slug mass and leaf consumption by A. vulgaris. At the third trophic level, plants infested with slugs and plants co-infested with slugs and caterpillars were far less attractive to parasitoids than plants damaged by caterpillars only, independently of slug species. Chemical analyses confirmed that volatile emissions, which provide foraging cues for parasitoids, were strongly reduced in co-infested plants. Our study shows that the presence of slugs has the potential to affect insect populations, directly via consumptive effects, and indirectly via changes in plant volatiles that result in a reduced attraction of natural enemies. The fitness cost for P. brassicae imposed by increased mortality in presence of slugs may be counterbalanced by the benefit of escaping its parasitoids.

Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus.

PubMed

Cheng, Hongtao; Hao, Mengyu; Wang, Wenxiang; Mei, Desheng; Tong, Chaobo; Wang, Hui; Liu, Jia; Fu, Li; Hu, Qiong

2016-09-08

SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined. In the present study, by whole genome bioinformatics analysis and transcriptional profiling, 58 putative members of SBP-box gene family in oilseed rape (Brassica napus L.) were identified and their expression pattern in different tissues as well as possible interaction with miRNAs were analyzed. In addition, B. napus lines with contrasting branch angle were used for investigating the involvement of SBP-box genes in plant architecture regulation. Detailed gene information, including genomic organization, structural feature, conserved domain and phylogenetic relationship of the genes were systematically characterized. By phylogenetic analysis, BnaSBP proteins were classified into eight distinct groups representing the clear orthologous relationships to their family members in Arabidopsis and rice. Expression analysis in twelve tissues including vegetative and reproductive organs showed different expression patterns among the SBP-box genes and a number of the genes exhibit tissue specific expression, indicating their diverse functions involved in the developmental process. Forty-four SBP-box genes were ascertained to contain the putative miR156 binding site, with 30 and 14 of the genes targeted by miR156 at the coding and 3'UTR region, respectively. Relative expression level of miR156 is varied across tissues. Different expression pattern of some BnaSBP genes and the negative correlation of transcription levels between miR156 and its target BnaSBP gene were observed in lines with different branch angle. Taken together, this study represents the first systematic analysis of the SBP-box gene family in Brassica napus. The data presented here provides base foundation for

NMR metabolomics of ripened and developing oilseed rape (Brassica napus) and turnip rape (Brassica rapa).

PubMed

Kortesniemi, Maaria; Vuorinen, Anssi L; Sinkkonen, Jari; Yang, Baoru; Rajala, Ari; Kallio, Heikki

2015-04-01

The oilseeds of the commercially important oilseed rape (Brassica napus) and turnip rape (Brassica rapa) were investigated with (1)H NMR metabolomics. The compositions of ripened (cultivated in field trials) and developing seeds (cultivated in controlled conditions) were compared in multivariate models using principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and orthogonal partial least squares discriminant analysis (OPLS-DA). Differences in the major lipids and the minor metabolites between the two species were found. A higher content of polyunsaturated fatty acids and sucrose were observed in turnip rape, while the overall oil content and sinapine levels were higher in oilseed rape. The genotype traits were negligible compared to the effect of the growing site and concomitant conditions on the oilseed metabolome. This study demonstrates the applicability of NMR-based analysis in determining the species, geographical origin, developmental stage, and quality of oilseed Brassicas. Copyright © 2014 Elsevier Ltd. All rights reserved.

Intracellular Ca(2+) and K(+) concentration in Brassica oleracea leaf induces differential expression of transporter and stress-related genes.

PubMed

Lee, Jeongyeo; Kim, Jungeun; Choi, Jae-Pil; Lee, MiYe; Kim, Min Keun; Lee, Young Han; Hur, Yoonkang; Nou, Ill-Sup; Park, Sang Un; Min, Sung Ran; Kim, HyeRan

2016-03-09

One of the most important members of the genus Brassica, cabbage, requires a relatively high level of calcium for normal growth (Plant Cell Environ 7: 397-405, 1984; Plant Physiol 60: 854-856, 1977). Localized Ca(2+) deficiency in cabbage leaves causes tip-burn, bringing about serious economic losses (Euphytica 9:203-208, 1960; Ann Bot 43:363-372, 1979; Sci Hortic 14:131-138, 1981). Although it has been known that the occurrence of tip-burn is related to Ca(2+) deficiency, there is limited information on the underlying mechanisms of tip-burn or the relationship between Ca(2+) and tip-burn incidence. To obtain more information on the genetic control of tip-burn symptoms, we focused on the identification of genes differentially expressed in response to increasing intracellular Ca(2+) and K(+) concentrations in B. oleracea lines derived from tip-burn susceptible, tip-burn resistant cabbages (B. oleracea var. capitata), and kale (B. oleracea var. acephala). We compared the levels of major macronutrient cations, including Ca(2+) and K(+), in three leaf segments, the leaf apex (LA), middle of leaf (LM), and leaf base (LB), of tip-burn susceptible, tip-burn resistant cabbages, and kale. Ca(2+) and K(+) concentrations were highest in kale, followed by tip-burn resistant and then tip-burn susceptible cabbages. These cations generally accumulated to a greater extent in the LB than in the LA. Transcriptome analysis identified 58,096 loci as putative non-redundant genes in the three leaf segments of the three B. oleracea lines and showed significant changes in expression of 27,876 loci based on Ca(2+) and K(+) levels. Among these, 1844 loci were identified as tip-burn related phenotype-specific genes. Tip-burn resistant cabbage and kale-specific genes were largely related to stress and transport activity based on GO annotation. Tip-burn resistant cabbage and kale plants showed phenotypes clearly indicative of heat-shock, freezing, and drought stress tolerance compared to tip

Functional identification of genes responsible for the biosynthesis of 1-methoxy-indol-3-ylmethyl-glucosinolate in Brassica rapa ssp. chinensis

PubMed Central

2014-01-01

Background Brassica vegetables contain a class of secondary metabolites, the glucosinolates (GS), whose specific degradation products determine the characteristic flavor and smell. While some of the respective degradation products of particular GS are recognized as health promoting substances for humans, recent studies also show evidence that namely the 1-methoxy-indol-3-ylmethyl GS might be deleterious by forming characteristic DNA adducts. Therefore, a deeper knowledge of aspects involved in the biosynthesis of indole GS is crucial to design vegetables with an improved secondary metabolite profile. Results Initially the leafy Brassica vegetable pak choi (Brassica rapa ssp. chinensis) was established as suitable tool to elicit very high concentrations of 1-methoxy-indol-3-ylmethyl GS by application of methyl jasmonate. Differentially expressed candidate genes were discovered in a comparative microarray analysis using the 2 × 104 K format Brassica Array and compared to available gene expression data from the Arabidopsis AtGenExpress effort. Arabidopsis knock out mutants of the respective candidate gene homologs were subjected to a comprehensive examination of their GS profiles and confirmed the exclusive involvement of polypeptide 4 of the cytochrome P450 monooxygenase subfamily CYP81F in 1-methoxy-indol-3-ylmethyl GS biosynthesis. Functional characterization of the two identified isoforms coding for CYP81F4 in the Brassica rapa genome was performed using expression analysis and heterologous complementation of the respective Arabidopsis mutant. Conclusions Specific differences discovered in a comparative microarray and glucosinolate profiling analysis enables the functional attribution of Brassica rapa ssp. chinensis genes coding for polypeptide 4 of the cytochrome P450 monooxygenase subfamily CYP81F to their metabolic role in indole glucosinolate biosynthesis. These new identified Brassica genes will enable the development of genetic tools for breeding

The response of transgenic Brassica species to salt stress: a review.

PubMed

Shah, Nadil; Anwar, Sumera; Xu, Jingjing; Hou, Zhaoke; Salah, Akram; Khan, Shahbaz; Gong, Jianfang; Shang, Zhengwei; Qian, Li; Zhang, Chunyu

2018-06-01

Salt stress is considered one of the main abiotic factors to limit crop growth and productivity by affecting morpho-physiological and biochemical processes. Genetically, a number of salt tolerant Brassica varieties have been developed and introduced, but breeding of such varieties is time consuming. Therefore, current focus is on transgenic technology, which plays an important role in the development of salt tolerant varieties. Various salt tolerant genes have been characterized and incorporated into Brassica. Therefore, such genetic transformation of Brassica species is a significant step for improvement of crops, as well as conferring salt stress resistance qualities to Brassica species. Complete genome sequencing has made the task of genetically transforming Brassica species easier, by identifying desired candidate genes. The present review discusses relevant information about the principles which should be employed to develop transgenic Brassica species, and also will recommend tools for improved tolerance to salinity.

Identification of Isolates that Cause a Leaf Spot Disease of Brassicas as Xanthomonas campestris pv. raphani and Pathogenic and Genetic Comparison with Related Pathovars.

PubMed

Vicente, J G; Everett, B; Roberts, S J

2006-07-01

ABSTRACT Twenty-five Xanthomonas isolates, including some isolates received as either X. campestris pv. armoraciae or pv. raphani, caused discrete leaf spot symptoms when spray-inoculated onto at least one Brassica oleracea cultivar. Twelve of these isolates and four other Xanthomonas isolates were spray- and pin-inoculated onto 21 different plant species/cultivars including horseradish (Armoracia rusticana), radish (Raphanus sativus), and tomato (Lycopersicon esculentum). The remaining 13 leaf spot isolates were spray-inoculated onto a subset of 10 plant species/cultivars. The leaf spot isolates were very aggressive on several Brassica spp., radish, and tomato causing leaf spots and dark sunken lesions on the middle vein, petiole, and stem. Based on the differential reactions of several Brassica spp. and radish cultivars, the leaf spot isolates were divided into three races, with races 1 and 3 predominating. A differential series was established to determine the race-type of isolates and a gene-for-gene model based on the interaction of two avirulence genes in the pathogen races and two matching resistance genes in the differential hosts is proposed. Repetitive-DNA polymerase chain reaction-based fingerprinting was used to assess the genetic diversity of the leaf spot isolates and isolates of closely related Xanthomonas pathovars. Although there was variability within each race, the leaf spot isolates were clustered separately from the X. campestris pv. campestris isolates. We propose that X. campestris isolates that cause a nonvascular leaf spot disease on Brassica spp. should be identified as pv. raphani and not pv. armoraciae. Race-type strains and a neopathotype strain for X. campestris pv. raphani are proposed.

A Method to Teach Age-Specific Demography with Field Grown Rapid Cycling "Brassica rapa" (Wisconsin Fast Plants)

ERIC Educational Resources Information Center

Kelly, Martin G.; Terrana, Sebastian

2004-01-01

In this paper, we demonstrate that rapid cycling "Brassica rapa" (Wisconsin Fast Plants) can be used in inquiry-based, student ecological fieldwork. We are the first to describe age-specific survival for field-grown Fast Plants and identify life history traits associated with individual survival. This experiment can be adapted by educators as a…

Brassica oleracea: the dog of the plant world

USDA-ARS?s Scientific Manuscript database

The horticultural crop Brassica oleracea L. plays an important role in global food systems. Brassica oleracea is unique in that it has been domesticated into several morphotypes (cultivars), including broccoli, Brussels sprout, cabbage, cauliflower, kale, kohlrabi, and several lesser well known morp...

Brassica oleracea; The dog of the plant world

USDA-ARS?s Scientific Manuscript database

The horticultural crop Brassica oleracea L. plays an important role in global food systems. Brassica oleracea is unique in that it has been domesticated into several morphotypes (cultivars), including broccoli, Brussels sprout, cabbage, cauliflower, kale, kohlrabi, and several lesser well known morp...

Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica.

PubMed

Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

2015-01-01

Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the "candidate genes" and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops.

Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica

PubMed Central

Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

2015-01-01

Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the “candidate genes” and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops. PMID:26388887

Examining the impact of differential cultural adaptation with Latina/o immigrants exposed to adapted parent training interventions

PubMed Central

Parra-Cardona, J. Rubén; Bybee, Deborah; Sullivan, Cris M.; Domenech Rodríguez, Melanie M.; Dates, Brian; Tams, Lisa; Bernal, Guillermo

2016-01-01

Objective There is a dearth of empirical studies aimed at examining the impact of differential cultural adaptation of evidence-based clinical and prevention interventions. This prevention study consisted of a randomized controlled trial aimed at comparing the impact of two differentially culturally adapted versions of the evidence-based parenting intervention known as Parent Management Training, the Oregon Model (PMTOR). Method The sample consisted of 103 Latina/o immigrant families (190 individual parents). Each family was allocated to one of three conditions: (a) a culturally adapted PMTO (CA), (b) culturally adapted and enhanced PMTO (CE), and (c) a wait-list control. Measurements were implemented at baseline (T1), treatment completion (T2) and 6-month follow up (T3). Results Multi-level growth modeling analyses indicated statistically significant improvements on parenting skills for fathers and mothers (main effect) at 6-month follow-up in both adapted interventions, when compared to the control condition. With regards to parent-reported child behaviors, child internalizing behaviors were significantly lower for both parents in the CE intervention (main effect), compared with control at 6-month follow-up. No main effect was found for child externalizing behaviors. However, a Parent x Condition effect was found indicating a significant reduction of child externalizing behaviors for CE fathers compared to CA and control fathers at posttest and 6-month follow-up. Conclusion Present findings indicate the value of differential cultural adaptation research designs and the importance of examining effects for both mothers and fathers, particularly when culturally-focused and gender variables are considered for intervention design and implementation. PMID:28045288

Simultaneous detection and differentiation of three genotypes of Brassica yellows virus by multiplex reverse transcription-polymerase chain reaction.

PubMed

Zhang, Xiaoyan; Peng, Yanmei; Wang, Ying; Zhang, Zongying; Li, Dawei; Yu, Jialin; Han, Chenggui

2016-11-22

Brassica yellows virus (BrYV), proposed to be a new polerovirus species, three distinct genotypes (BrYV-A, BrYV-B and BrYV-C) have been described. This study was to develop a simple, rapid, sensitive, cost-effective method for simultaneous detection and differentiation of three genotypes of BrYV. In this study, a multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for simultaneous detection and differentiation of the three genotypes of BrYV. The three genotypes of BrYV and Tunip yellows virus (TuYV) could be differentiated simultaneously using six optimized specific oligonucleotide primers, including one universal primer for detecting BrYV, three BrYV genotype-specific primers, and a pair of primers for specific detection of TuYV. Primers were designed from conserved regions of each virus and their specificity was confirmed by sequencing PCR products. The mRT-PCR products were 278 bp for BrYV-A, 674 bp for BrYV-B, 505 bp for BrYV-C, and 205 bp for TuYV. Amplification of three target genotypes was optimized by increasing the PCR annealing temperatures to 62 °C. One to three fragments specific for the virus genotypes were simultaneously amplified from infected samples and identified by their specific molecular sizes in agarose gel electrophoresis. No specific products could be amplified from cDNAs of other viruses which could infect crucifer crops. Detection limits of the plasmids for multiplex PCR were 100 fg for BrYV-A and BrYV-B, 10 pg for BrYV-C, and 1 pg for TuYV, respectively. The mRT-PCR was applied successfully for detection of three BrYV genotypes from field samples collected in China. The simple, rapid, sensitive, and cost-effective mRT-PCR was developed successfully for detection and differentiation of the three genotypes of BrYV.

Potential of forage brassicas for use in pasture-based livestock systems

USDA-ARS?s Scientific Manuscript database

Brassicas (Brassica spp.) are gaining popularity as high-quality forage for pasture-based livestock producers due to their use to extend the fall grazing season and during the summer forage slump. However, inclusion of brassicas in the diet can be limited by the presence of glucosinolates (a class o...

Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species

PubMed Central

Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

2014-01-01

Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species. PMID:24130371

Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species.

PubMed

Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

2014-02-01

Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.

Solving delay differential equations in S-ADAPT by method of steps.

PubMed

Bauer, Robert J; Mo, Gary; Krzyzanski, Wojciech

2013-09-01

S-ADAPT is a version of the ADAPT program that contains additional simulation and optimization abilities such as parametric population analysis. S-ADAPT utilizes LSODA to solve ordinary differential equations (ODEs), an algorithm designed for large dimension non-stiff and stiff problems. However, S-ADAPT does not have a solver for delay differential equations (DDEs). Our objective was to implement in S-ADAPT a DDE solver using the methods of steps. The method of steps allows one to solve virtually any DDE system by transforming it to an ODE system. The solver was validated for scalar linear DDEs with one delay and bolus and infusion inputs for which explicit analytic solutions were derived. Solutions of nonlinear DDE problems coded in S-ADAPT were validated by comparing them with ones obtained by the MATLAB DDE solver dde23. The estimation of parameters was tested on the MATLB simulated population pharmacodynamics data. The comparison of S-ADAPT generated solutions for DDE problems with the explicit solutions as well as MATLAB produced solutions which agreed to at least 7 significant digits. The population parameter estimates from using importance sampling expectation-maximization in S-ADAPT agreed with ones used to generate the data. Published by Elsevier Ireland Ltd.

Oscillatory stimuli differentiate adapting circuit topologies

PubMed Central

Rahi, Sahand Jamal; Larsch, Johannes; Pecani, Kresti; Katsov, Alexander Y.; Mansouri, Nahal; Tsaneva-Atanasova, Krasimira; Sontag, Eduardo D.; Cross, Frederick R.

2017-01-01

Adapting pathways consist of negative feedback loops (NFLs) or incoherent feedforward loops (IFFLs), which we show can be differentiated using oscillatory stimulation: NFLs but not IFFLs generically show ‘refractory period stabilization’ or ‘period skipping’. Using these signatures and genetic rewiring we identified the circuit dominating cell cycle timing in yeast. In C. elegans AWA neurons we uncovered a Ca2+-NFL, diffcult to find by other means, especially in wild-type, intact animals. (70 words) PMID:28846089

Feed mechanism and method for feeding minute items

DOEpatents

Stringer, Timothy Kent; Yerganian, Simon Scott

2012-11-06

A feeding mechanism and method for feeding minute items, such as capacitors, resistors, or solder preforms. The mechanism is adapted to receive a plurality of the randomly-positioned and randomly-oriented extremely small or minute items, and to isolate, orient, and position the items in a specific repeatable pickup location wherefrom they may be removed for use by, for example, a computer-controlled automated assembly machine. The mechanism comprises a sliding shelf adapted to receive and support the items; a wiper arm adapted to achieve a single even layer of the items; and a pushing arm adapted to push the items into the pickup location. The mechanism can be adapted for providing the items with a more exact orientation, and can also be adapted for use in a liquid environment.

Feed mechanism and method for feeding minute items

DOEpatents

Stringer, Timothy Kent [Bucyrus, KS; Yerganian, Simon Scott [Lee's Summit, MO

2009-10-20

A feeding mechanism and method for feeding minute items, such as capacitors, resistors, or solder preforms. The mechanism is adapted to receive a plurality of the randomly-positioned and randomly-oriented extremely small or minute items, and to isolate, orient, and position one or more of the items in a specific repeatable pickup location wherefrom they may be removed for use by, for example, a computer-controlled automated assembly machine. The mechanism comprises a sliding shelf adapted to receive and support the items; a wiper arm adapted to achieve a single even layer of the items; and a pushing arm adapted to push the items into the pickup location. The mechanism can be adapted for providing the items with a more exact orientation, and can also be adapted for use in a liquid environment.

Reduction of antinutritional glucosinolates in Brassica oilseeds by mutation of genes encoding transporters.

PubMed

Nour-Eldin, Hussam Hassan; Madsen, Svend Roesen; Engelen, Steven; Jørgensen, Morten Egevang; Olsen, Carl Erik; Andersen, Jonathan Sonne; Seynnaeve, David; Verhoye, Thalia; Fulawka, Rudy; Denolf, Peter; Halkier, Barbara Ann

2017-04-01

The nutritional value of Brassica seed meals is reduced by the presence of glucosinolates, which are toxic compounds involved in plant defense. Mutation of the genes encoding two glucosinolate transporters (GTRs) eliminated glucosinolates from Arabidopsis thaliana seeds, but translation of loss-of-function phenotypes into Brassica crops is challenging because Brassica is polyploid. We mutated one of seven and four of 12 GTR orthologs and reduced glucosinolate levels in seeds by 60-70% in two different Brassica species (Brassica rapa and Brassica juncea). Reduction in seed glucosinolates was stably inherited over multiple generations and maintained in field trials of two mutant populations at three locations. Successful translation of the gtr loss-of-function phenotype from model plant to two Brassica crops suggests that our transport engineering approach could be broadly applied to reduce seed glucosinolate content in other oilseed crops, such as Camelina sativa or Crambe abyssinica.

Examining the impact of differential cultural adaptation with Latina/o immigrants exposed to adapted parent training interventions.

PubMed

Parra-Cardona, J Rubén; Bybee, Deborah; Sullivan, Cris M; Rodríguez, Melanie M Domenech; Dates, Brian; Tams, Lisa; Bernal, Guillermo

2017-01-01

There is a dearth of empirical studies aimed at examining the impact of differential cultural adaptation of evidence-based clinical and prevention interventions. This prevention study consisted of a randomized controlled trial aimed at comparing the impact of 2 differentially culturally adapted versions of the evidence-based parenting intervention known as Parent Management Training, the Oregon Model (PMTOR). The sample consisted of 103 Latina/o immigrant families (190 individual parents). Each family was allocated to 1 of 3 conditions: (a) a culturally adapted PMTO (CA), (b) culturally adapted and enhanced PMTO (CE), and (c) a wait-list control. Measurements were implemented at baseline (T1), treatment completion (T2) and 6-month follow up (T3). Multilevel growth modeling analyses indicated statistically significant improvements on parenting skills for fathers and mothers (main effect) at 6-month follow-up in both adapted interventions, when compared with the control condition. With regard to parent-reported child behaviors, child internalizing behaviors were significantly lower for both parents in the CE intervention (main effect), compared with control at 6-month follow-up. No main effect was found for child externalizing behaviors. However, a Parent × Condition effect was found indicating a significant reduction of child externalizing behaviors for CE fathers compared with CA and control fathers at posttest and 6-month follow-up. Present findings indicate the value of differential cultural adaptation research designs and the importance of examining effects for both mothers and fathers, particularly when culturally focused and gender variables are considered for intervention design and implementation. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Identification and characterization of mobile genetic elements LINEs from Brassica genome.

PubMed

Nouroz, Faisal; Noreen, Shumaila; Khan, Muhammad Fiaz; Ahmed, Shehzad; Heslop-Harrison, J S Pat

2017-09-05

Among transposable elements (TEs), the LTR retrotransposons are abundant followed by non-LTR retrotransposons in plant genomes, the lateral being represented by LINEs and SINEs. Computational and molecular approaches were used for the characterization of Brassica LINEs, their diversity and phylogenetic relationships. Four autonomous and four non-autonomous LINE families were identified and characterized from Brassica. Most of the autonomous LINEs displayed two open reading frames, ORF1 and ORF2, where ORF1 is a gag protein domain, while ORF2 encodes endonuclease (EN) and a reverse transcriptase (RT). Three of four families encoded an additional RNase H (RH) domain in pol gene common to 'R' and 'I' type of LINEs. The PCR analyses based on LINEs RT fragments indicate their high diversity and widespread occurrence in tested 40 Brassica cultivars. Database searches revealed the homology in LINE sequences in closely related genera Arabidopsis indicating their origin from common ancestors predating their separation. The alignment of 58 LINEs RT sequences from Brassica, Arabidopsis and other plants depicted 4 conserved domains (domain II-V) showing similarity to previously detected domains. Based on RT alignment of Brassica and 3 known LINEs from monocots, Brassicaceae LINEs clustered in separate clade, further resolving 4 Brassica-Arabidopsis specific families in 2 sub-clades. High similarities were observed in RT sequences in the members of same family, while low homology was detected in members across the families. The investigation led to the characterization of Brassica specific LINE families and their diversity across Brassica species and their cultivars. Copyright © 2017 Elsevier B.V. All rights reserved.

Small RNA Sequencing Reveals Differential miRNA Expression in the Early Development of Broccoli (Brassica oleracea var. italica) Pollen

PubMed Central

Li, Hui; Wang, Yu; Wu, Mei; Li, Lihong; Jin, Chuan; Zhang, Qingli; Chen, Chengbin; Song, Wenqin; Wang, Chunguo

2017-01-01

Pollen development is an important and complex biological process in the sexual reproduction of flowering plants. Although the cytological characteristics of pollen development are well defined, the regulation of its early stages remains largely unknown. In the present study, miRNAs were explored in the early development of broccoli (Brassica oleracea var. italica) pollen. A total of 333 known miRNAs that originated from 235 miRNA families were detected. Fifty-five novel miRNA candidates were identified. Sixty of the 333 known miRNAs and 49 of the 55 predicted novel miRNAs exhibited significantly differential expression profiling in the three distinct developmental stages of broccoli pollen. Among these differentially expressed miRNAs, miRNAs that would be involved in the developmental phase transition from uninucleate microspores to binucleate pollen grains or from binucleate to trinucleate pollen grains were identified. miRNAs that showed significantly enriched expression in a specific early stage of broccoli pollen development were also observed. In addition, 552 targets for 127 known miRNAs and 69 targets for 40 predicted novel miRNAs were bioinformatically identified. Functional annotation and GO (Gene Ontology) analysis indicated that the putative miRNA targets showed significant enrichment in GO terms that were related to plant organ formation and morphogenesis. Some of enriched GO terms were detected for the targets directly involved in plant male reproduction development. These findings provided new insights into the functions of miRNA-mediated regulatory networks in broccoli pollen development. PMID:28392797

Small RNA Sequencing Reveals Differential miRNA Expression in the Early Development of Broccoli (Brassica oleracea var. italica) Pollen.

PubMed

Li, Hui; Wang, Yu; Wu, Mei; Li, Lihong; Jin, Chuan; Zhang, Qingli; Chen, Chengbin; Song, Wenqin; Wang, Chunguo

2017-01-01

Pollen development is an important and complex biological process in the sexual reproduction of flowering plants. Although the cytological characteristics of pollen development are well defined, the regulation of its early stages remains largely unknown. In the present study, miRNAs were explored in the early development of broccoli ( Brassica oleracea var. italica ) pollen. A total of 333 known miRNAs that originated from 235 miRNA families were detected. Fifty-five novel miRNA candidates were identified. Sixty of the 333 known miRNAs and 49 of the 55 predicted novel miRNAs exhibited significantly differential expression profiling in the three distinct developmental stages of broccoli pollen. Among these differentially expressed miRNAs, miRNAs that would be involved in the developmental phase transition from uninucleate microspores to binucleate pollen grains or from binucleate to trinucleate pollen grains were identified. miRNAs that showed significantly enriched expression in a specific early stage of broccoli pollen development were also observed. In addition, 552 targets for 127 known miRNAs and 69 targets for 40 predicted novel miRNAs were bioinformatically identified. Functional annotation and GO (Gene Ontology) analysis indicated that the putative miRNA targets showed significant enrichment in GO terms that were related to plant organ formation and morphogenesis. Some of enriched GO terms were detected for the targets directly involved in plant male reproduction development. These findings provided new insights into the functions of miRNA-mediated regulatory networks in broccoli pollen development.

Differential face-network adaptation in children, adolescents and adults.

PubMed

Cohen Kadosh, Kathrin; Johnson, Mark H; Henson, Richard N A; Dick, Frederic; Blakemore, Sarah-Jayne

2013-04-01

Faces are complex social stimuli, which can be processed both at the categorical and the individual level. Behavioral studies have shown that children take more than a decade of exposure and training to become proficient at processing faces at the individual level. The neurodevelopmental trajectories for different aspects of face-processing are still poorly understood. In this study, we used an fMR-adaptation design to investigate differential processing of three face aspects (identity, expression and gaze) in children, adolescents and adults. We found that, while all three tasks showed some overlap in activation patterns, there was a significant age effect in the occipital and temporal lobes and the inferior frontal gyrus. More importantly, the degree of adaptation differed across the three age groups in the inferior occipital gyrus, a core face processing area that has been shown in previous studies to be both integral and necessary for individual-level face processing. In the younger children, adaptation in this region seemed to suggest the use of a predominantly featural processing strategy, whereas adaptation effects in the adults exhibited a more strategic pattern that depended on the task. Interestingly, our sample of adolescents did not exhibit any differential adaptation effects; possibly reflecting increased heterogeneity in processing strategies in this age group. Our results support the notion that, in line with improving behavioral face-processing abilities, core face-responsive regions develop throughout the first two decades of life. Copyright © 2012 Elsevier Inc. All rights reserved.

Analysis of global gene expression profiles to identify differentially expressed genes critical for embryo development in Brassica rapa.

PubMed

Zhang, Yu; Peng, Lifang; Wu, Ya; Shen, Yanyue; Wu, Xiaoming; Wang, Jianbo

2014-11-01

Embryo development represents a crucial developmental period in the life cycle of flowering plants. To gain insights into the genetic programs that control embryo development in Brassica rapa L., RNA sequencing technology was used to perform transcriptome profiling analysis of B. rapa developing embryos. The results generated 42,906,229 sequence reads aligned with 32,941 genes. In total, 27,760, 28,871, 28,384, and 25,653 genes were identified from embryos at globular, heart, early cotyledon, and mature developmental stages, respectively, and analysis between stages revealed a subset of stage-specific genes. We next investigated 9,884 differentially expressed genes with more than fivefold changes in expression and false discovery rate ≤ 0.001 from three adjacent-stage comparisons; 1,514, 3,831, and 6,633 genes were detected between globular and heart stage embryo libraries, heart stage and early cotyledon stage, and early cotyledon and mature stage, respectively. Large numbers of genes related to cellular process, metabolism process, response to stimulus, and biological process were expressed during the early and middle stages of embryo development. Fatty acid biosynthesis, biosynthesis of secondary metabolites, and photosynthesis-related genes were expressed predominantly in embryos at the middle stage. Genes for lipid metabolism and storage proteins were highly expressed in the middle and late stages of embryo development. We also identified 911 transcription factor genes that show differential expression across embryo developmental stages. These results increase our understanding of the complex molecular and cellular events during embryo development in B. rapa and provide a foundation for future studies on other oilseed crops.

Identification and compensation of friction for a novel two-axis differential micro-feed system

NASA Astrophysics Data System (ADS)

Du, Fuxin; Zhang, Mingyang; Wang, Zhaoguo; Yu, Chen; Feng, Xianying; Li, Peigang

2018-06-01

Non-linear friction in a conventional drive feed system (CDFS) feeding at low speed is one of the main factors that lead to the complexity of the feed drive. The CDFS will inevitably enter or approach a non-linear creeping work area at extremely low speed. A novel two-axis differential micro-feed system (TDMS) is developed in this paper to overcome the accuracy limitation of CDFS. A dynamic model of TDMS is first established. Then, a novel all-component friction parameter identification method (ACFPIM) using a genetic algorithm (GA) to identify the friction parameters of a TDMS is introduced. The friction parameters of the ball screw and linear motion guides are identified independently using the method, assuring the accurate modelling of friction force at all components. A proportional-derivate feed drive position controller with an observer-based friction compensator is implemented to achieve an accurate trajectory tracking performance. Finally, comparative experiments demonstrate the effectiveness of the TDMS in inhibiting the disadvantageous influence of non-linear friction and the validity of the proposed identification method for TDMS.

Detecting consistent patterns of directional adaptation using differential selection codon models.

PubMed

Parto, Sahar; Lartillot, Nicolas

2017-06-23

Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors. However, some organisms may be subject to systematic changes in selective pressure, resulting in reproducible molecular adaptations across independent lineages subject to similar conditions. Here, we introduce a codon-based differential selection model, which aims to detect and quantify the fine-grained consistent patterns of adaptation at the protein-coding level, as a function of external conditions experienced by the organism under investigation. The model parameterizes the global mutational pressure, as well as the site- and condition-specific amino acid selective preferences. This phylogenetic model is implemented in a Bayesian MCMC framework. After validation with simulations, we applied our method to a dataset of HIV sequences from patients with known HLA genetic background. Our differential selection model detects and characterizes differentially selected coding positions specifically associated with two different HLA alleles. Our differential selection model is able to identify consistent molecular adaptations as a function of repeated changes in the environment of the organism. These models can be applied to many other problems, ranging from viral adaptation to evolution of life-history strategies in plants or animals.

Identification and Characterization of Crr1a, a Gene for Resistance to Clubroot Disease (Plasmodiophora brassicae Woronin) in Brassica rapa L.

PubMed Central

Hatakeyama, Katsunori; Suwabe, Keita; Tomita, Rubens Norio; Kato, Takeyuki; Nunome, Tsukasa; Fukuoka, Hiroyuki; Matsumoto, Satoru

2013-01-01

Clubroot disease, caused by the obligate biotrophic protist Plasmodiophora brassicae Woronin, is one of the most economically important diseases of Brassica crops in the world. Although many clubroot resistance (CR) loci have been identified through genetic analysis and QTL mapping, the molecular mechanisms of defense responses against P. brassicae remain unknown. Fine mapping of the Crr1 locus, which was originally identified as a single locus, revealed that it comprises two gene loci, Crr1a and Crr1b. Here we report the map-based cloning and characterization of Crr1a, which confers resistance to clubroot in Brassica rapa. Crr1aG004, cloned from the resistant line G004, encodes a Toll-Interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat (TIR-NB-LRR) protein expressed in the stele and cortex of hypocotyl and roots, where secondary infection of the pathogen occurs, but not in root hairs, where primary infection occurs. Gain-of-function analysis proved that Crr1aG004 alone conferred resistance to isolate Ano-01 in susceptible Arabidopsis and B. rapa. In comparison, the susceptible allele Crr1aA9709 encodes a truncated NB-LRR protein, which lacked more than half of the TIR domain on account of the insertion of a solo-long terminal repeat (LTR) in exon 1 and included several substitutions and insertion-deletions in the LRR domain. This study provides a basis for further molecular analysis of defense mechanisms against P. brassicae and will contribute to the breeding of resistant cultivars of Brassica vegetables by marker-assisted selection. Data deposition The sequence reported in this paper has been deposited in the GenBank database (accession no. AB605024). PMID:23382954

Cadmium phytoremediation potential of Brassica crop species: A review.

PubMed

Rizwan, Muhammad; Ali, Shafaqat; Zia Ur Rehman, Muhammad; Rinklebe, Jörg; Tsang, Daniel C W; Bashir, Arooj; Maqbool, Arosha; Tack, F M G; Ok, Yong Sik

2018-08-01

Cadmium (Cd) is a highly toxic metal released into the environment through anthropogenic activities. Phytoremediation is a green technology used for the stabilization or remediation of Cd-contaminated soils. Brassica crop species can produce high biomass under a range of climatic and growing conditions, allowing for considerable uptake and accumulation of Cd, depending on species. These crop species can tolerate Cd stress via different mechanisms, including the stimulation of the antioxidant defense system, chelation, compartmentation of Cd into metabolically inactive parts, and accumulation of total amino-acids and osmoprotectants. A higher Cd-stress level, however, overcomes the defense system and may cause oxidative stress in Brassica species due to overproduction of reactive oxygen species and lipid peroxidation. Therefore, numerous approaches have been followed to decrease Cd toxicity in Brassica species, including selection of Cd-tolerant cultivars, the use of inorganic and organic amendments, exogenous application of soil organisms, and employment of plant-growth regulators. Furthermore, the coupling of genetic engineering with cropping may also help to alleviate Cd toxicity in Brassica species. However, several field studies demonstrated contrasting results. This review suggests that the combination of Cd-tolerant Brassica cultivars and the application of soil amendments, along with proper agricultural practices, may be the most efficient means of the soil Cd phytoattenuation. Breeding and selection of Cd-tolerant species, as well as species with higher biomass production, might be needed in the future when aiming to use Brassica species for phytoremediation. Copyright © 2018 Elsevier B.V. All rights reserved.

Morphological integration and pleiotropy in the adaptive body shape of the snail-feeding carabid beetle Damaster blaptoides.

PubMed

Konuma, Junji; Yamamoto, Satoshi; Sota, Teiji

2014-12-01

The snail-feeding carabid beetle Damaster blaptoides exhibits diverse head and thorax morphologies, and these morphotypes are linked with two alternative feeding behaviours. Stout-shaped beetles feed on snails by crushing the shells, whereas slender-shaped beetles consume snails by inserting their heads into the shells. A trade-off exists between these feeding strategies. Because intermediate-shaped beetles are less proficient in these two behaviours, stout-slender morphological divergence occurs between related species feeding on land snails. To examine the genetic basis of these morphotypes, we conducted morphological analyses and quantitative trait locus (QTL) mapping using backcross offspring between the stout and slender subspecies. The morphological analyses showed that the width and length of the beetle body parts were correlated with each other; in particular, the head width (HW) and thorax length (TL) were strongly negatively correlated. QTL mapping showed that QTLs for HW and TL are located in close proximity to one another on the longest linkage group and that they have positive and negative additive genetic effects. Our results suggest that the adaptive phenotypic sets of a wide head and short thorax and a narrow head and long thorax are based on the closeness of these QTLs. Morphological integration between the head and thorax may play an important role in the adaptive divergence of these beetles. © 2014 John Wiley & Sons Ltd.

Transcriptome analysis of Brassica napus pod using RNA-Seq and identification of lipid-related candidate genes.

PubMed

Xu, Hai-Ming; Kong, Xiang-Dong; Chen, Fei; Huang, Ji-Xiang; Lou, Xiang-Yang; Zhao, Jian-Yi

2015-10-24

Brassica napus is an important oilseed crop. Dissection of the genetic architecture underlying oil-related biological processes will greatly facilitates the genetic improvement of rapeseed. The differential gene expression during pod development offers a snapshot on the genes responsible for oil accumulation in. To identify candidate genes in the linkage peaks reported previously, we used RNA sequencing (RNA-Seq) technology to analyze the pod transcriptomes of German cultivar Sollux and Chinese inbred line Gaoyou. The RNA samples were collected for RNA-Seq at 5-7, 15-17 and 25-27 days after flowering (DAF). Bioinformatics analysis was performed to investigate differentially expressed genes (DEGs). Gene annotation analysis was integrated with QTL mapping and Brassica napus pod transcriptome profiling to detect potential candidate genes in oilseed. Four hundred sixty five and two thousand, one hundred fourteen candidate DEGs were identified, respectively, between two varieties at the same stages and across different periods of each variety. Then, 33 DEGs between Sollux and Gaoyou were identified as the candidate genes affecting seed oil content by combining those DEGs with the quantitative trait locus (QTL) mapping results, of which, one was found to be homologous to Arabidopsis thaliana lipid-related genes. Intervarietal DEGs of lipid pathways in QTL regions represent important candidate genes for oil-related traits. Integrated analysis of transcriptome profiling, QTL mapping and comparative genomics with other relative species leads to efficient identification of most plausible functional genes underlying oil-content related characters, offering valuable resources for bettering breeding program of Brassica napus. This study provided a comprehensive overview on the pod transcriptomes of two varieties with different oil-contents at the three developmental stages.

Can narrow-bandwidth light from UV-A to green alter secondary plant metabolism and increase Brassica plant defenses against aphids?

PubMed

Rechner, Ole; Neugart, Susanne; Schreiner, Monika; Wu, Sasa; Poehling, Hans-Michael

2017-01-01

Light of different wavelengths is essential for plant growth and development. Short-wavelength radiation such as UV can shift the composition of flavonoids, glucosinolates, and other plant metabolites responsible for enhanced defense against certain herbivorous insects. The intensity of light-induced, metabolite-based resistance is plant- and insect species-specific and depends on herbivore feeding guild and specialization. The increasing use of light-emitting diodes (LEDs) in horticultural plant production systems in protected environments enables the creation of tailor-made light scenarios for improved plant cultivation and induced defense against herbivorous insects. In this study, broccoli (Brassica oleracea var. italica) plants were grown in a climate chamber under broad spectra photosynthetic active radiation (PAR) and were additionally treated with the following narrow-bandwidth light generated with LEDs: UV-A (365 nm), violet (420 nm), blue (470 nm), or green (515 nm). We determined the influence of narrow-bandwidth light on broccoli plant growth, secondary plant metabolism (flavonol glycosides and glucosinolates), and plant-mediated light effects on the performance and behavior of the specialized cabbage aphid Brevicoryne brassicae. Green light increased plant height more than UV-A, violet, or blue LED treatments. Among flavonol glycosides, specific quercetin and kaempferol glycosides were increased under violet light. The concentration of 3-indolylmethyl glucosinolate in plants was increased by UV-A treatment. B. brassicae performance was not influenced by the different light qualities, but in host-choice tests, B. brassicae preferred previously blue-illuminated plants (but not UV-A-, violet-, or green-illuminated plants) over control plants.

Can narrow-bandwidth light from UV-A to green alter secondary plant metabolism and increase Brassica plant defenses against aphids?

PubMed Central

Neugart, Susanne; Schreiner, Monika; Wu, Sasa; Poehling, Hans-Michael

2017-01-01

Light of different wavelengths is essential for plant growth and development. Short-wavelength radiation such as UV can shift the composition of flavonoids, glucosinolates, and other plant metabolites responsible for enhanced defense against certain herbivorous insects. The intensity of light-induced, metabolite-based resistance is plant- and insect species-specific and depends on herbivore feeding guild and specialization. The increasing use of light-emitting diodes (LEDs) in horticultural plant production systems in protected environments enables the creation of tailor-made light scenarios for improved plant cultivation and induced defense against herbivorous insects. In this study, broccoli (Brassica oleracea var. italica) plants were grown in a climate chamber under broad spectra photosynthetic active radiation (PAR) and were additionally treated with the following narrow-bandwidth light generated with LEDs: UV-A (365 nm), violet (420 nm), blue (470 nm), or green (515 nm). We determined the influence of narrow-bandwidth light on broccoli plant growth, secondary plant metabolism (flavonol glycosides and glucosinolates), and plant-mediated light effects on the performance and behavior of the specialized cabbage aphid Brevicoryne brassicae. Green light increased plant height more than UV-A, violet, or blue LED treatments. Among flavonol glycosides, specific quercetin and kaempferol glycosides were increased under violet light. The concentration of 3-indolylmethyl glucosinolate in plants was increased by UV-A treatment. B. brassicae performance was not influenced by the different light qualities, but in host-choice tests, B. brassicae preferred previously blue-illuminated plants (but not UV-A-, violet-, or green-illuminated plants) over control plants. PMID:29190278

Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass.

PubMed

Jueterbock, A; Franssen, S U; Bergmann, N; Gu, J; Coyer, J A; Reusch, T B H; Bornberg-Bauer, E; Olsen, J L

2016-11-01

Populations distributed across a broad thermal cline are instrumental in addressing adaptation to increasing temperatures under global warming. Using a space-for-time substitution design, we tested for parallel adaptation to warm temperatures along two independent thermal clines in Zostera marina, the most widely distributed seagrass in the temperate Northern Hemisphere. A North-South pair of populations was sampled along the European and North American coasts and exposed to a simulated heatwave in a common-garden mesocosm. Transcriptomic responses under control, heat stress and recovery were recorded in 99 RNAseq libraries with ~13 000 uniquely annotated, expressed genes. We corrected for phylogenetic differentiation among populations to discriminate neutral from adaptive differentiation. The two southern populations recovered faster from heat stress and showed parallel transcriptomic differentiation, as compared with northern populations. Among 2389 differentially expressed genes, 21 exceeded neutral expectations and were likely involved in parallel adaptation to warm temperatures. However, the strongest differentiation following phylogenetic correction was between the three Atlantic populations and the Mediterranean population with 128 of 4711 differentially expressed genes exceeding neutral expectations. Although adaptation to warm temperatures is expected to reduce sensitivity to heatwaves, the continued resistance of seagrass to further anthropogenic stresses may be impaired by heat-induced downregulation of genes related to photosynthesis, pathogen defence and stress tolerance. © 2016 John Wiley & Sons Ltd.

Multidimensional adaptive evolution of a feed-forward network and the illusion of compensation

PubMed Central

Bullaughey, Kevin

2016-01-01

When multiple substitutions affect a trait in opposing ways, they are often assumed to be compensatory, not only with respect to the trait, but also with respect to fitness. This type of compensatory evolution has been suggested to underlie the evolution of protein structures and interactions, RNA secondary structures, and gene regulatory modules and networks. The possibility for compensatory evolution results from epistasis. Yet if epistasis is widespread, then it is also possible that the opposing substitutions are individually adaptive. I term this possibility an adaptive reversal. Although possible for arbitrary phenotype-fitness mappings, it has not yet been investigated whether such epistasis is prevalent in a biologically-realistic setting. I investigate a particular regulatory circuit, the type I coherent feed-forward loop, which is ubiquitous in natural systems and is accurately described by a simple mathematical model. I show that such reversals are common during adaptive evolution, can result solely from the topology of the fitness landscape, and can occur even when adaptation follows a modest environmental change and the network was well adapted to the original environment. The possibility of adaptive reversals warrants a systems perspective when interpreting substitution patterns in gene regulatory networks. PMID:23289561

Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies.

PubMed

Shen, Yue; Liu, Mingzhe; Wang, Lili; Li, Zhuowei; Taylor, David C; Li, Zhixi; Zhang, Meng

2016-04-01

Caleosins are a class of Ca(2+) binding proteins that appear to be ubiquitous in plants. Some of the main proteins embedded in the lipid monolayer of lipid droplets, caleosins, play critical roles in the degradation of storage lipids during germination and in lipid trafficking. Some of them have been shown to have histidine-dependent peroxygenase activity, which is believed to participate in stress responses in Arabidopsis. In the model plant Arabidopsis thaliana, caleosins have been examined extensively. However, little is known on a genome-wide scale about these proteins in other members of the Brassicaceae. In this study, 51 caleosins in Brassica plants and Arabidopsis lyrata were investigated and analyzed in silico. Among them, 31 caleosins, including 7 in A. lyrata, 11 in Brassica oleracea and 13 in Brassica napus, are herein identified for the first time. Segmental duplication was the main form of gene expansion. Alignment, motif and phylogenetic analyses showed that Brassica caleosins belong to either the H-family or the L-family with different motif structures and physicochemical properties. Our findings strongly suggest that L-caleosins are evolved from H-caleosins. Predicted phosphorylation sites were differentially conserved in H-caleosin and L-caleosins, respectively. 'RY-repeat' elements and phytohormone-related cis-elements were identified in different caleosins, which suggest diverse physiological functions. Gene structure analysis indicated that most caleosins (38 out of 44) contained six exons and five introns and their intron phases were highly conserved. Structurally integrated caleosins, such as BrCLO3-3 and BrCLO4-2, showed high expression levels and may have important roles. Some caleosins, such as BrCLO2 and BoCLO8-2, lost motifs of the calcium binding domain, proline knot, potential phosphorylation sites and haem-binding sites. Combined with their low expression, it is suggested that these caleosins may have lost function.

Redox state, reactive oxygen species and adaptive growth in colonial hydroids.

PubMed

Blackstone, N W

2001-06-01

Colonial metazoans often encrust surfaces over which the food supply varies in time or space. In such an environment, adaptive colony development entails adjusting the timing and spacing of feeding structures and gastrovascular connections to correspond to this variable food supply. To investigate the possibility of such adaptive growth, within-colony differential feeding experiments were carried out using the hydroid Podocoryna carnea. Indeed, such colonies strongly exhibited adaptive growth, developing dense arrays of polyps (feeding structures) and gastrovascular connections in areas that were fed relative to areas that were starved, and this effect became more consistent over time. To investigate mechanisms of signaling between the food supply and colony development, measurements were taken of metabolic parameters that have been implicated in signal transduction in other systems, particularly redox state and levels of reactive oxygen species. Utilizing fluorescence microscopy of P. carnea cells in vivo, simultaneous measurements of redox state [using NAD(P)H] and hydrogen peroxide (using 2',7'-dichlorofluorescin diacetate) were taken. Both measures focused on polyp epitheliomuscular cells, since these exhibit the greatest metabolic activity. Colonies 3-5h after feeding were relatively oxidized, with low levels of peroxide, while colonies 24h after feeding were relatively reduced, with high levels of peroxide. The functional role of polyps in feeding and generating gastrovascular flow probably produced this dichotomy. Polyps 3-5h after feeding contract maximally, and this metabolic demand probably shifts the redox state in the direction of oxidation and diminishes levels of reactive oxygen species. In contrast, 24h after feeding, polyps are quiescent, and this lack of metabolic demand probably shifts the redox state in the direction of reduction and increases levels of reactive oxygen species. Within-colony differential feeding experiments were carried out on

Impact of selenium supply on Se-methylselenocysteine and glucosinolate accumulation in selenium-biofortified Brassica sprouts.

PubMed

Avila, Fabricio William; Yang, Yong; Faquin, Valdemar; Ramos, Silvio Junio; Guilherme, Luiz Roberto G; Thannhauser, Theodore W; Li, Li

2014-12-15

Brassica sprouts are widely marketed as functional foods. Here we examined the effects of Se treatment on the accumulation of anticancer compound Se-methylselenocysteine (SeMSCys) and glucosinolates in Brassica sprouts. Cultivars from the six most extensively consumed Brassica vegetables (broccoli, cauliflower, green cabbage, Chinese cabbage, kale, and Brussels sprouts) were used. We found that Se-biofortified Brassica sprouts all were able to synthesize significant amounts of SeMSCys. Analysis of glucosinolate profiles revealed that each Brassica crop accumulated different types and amounts of glucosinolates. Cauliflower sprouts had high total glucosinolate content. Broccoli sprouts contained high levels of glucoraphanin, a precursor for potent anticancer compound. Although studies have reported an inverse relationship between accumulation of Se and glucosinolates in mature Brassica plants, Se supply generally did not affect glucosinolate accumulation in Brassica sprouts. Thus, Brassica vegetable sprouts can be biofortified with Se for the accumulation of SeMSCys without negative effects on chemopreventive glucosinolate contents. Published by Elsevier Ltd.

Population genomic analysis reveals differential evolutionary histories and patterns of diversity across subgenomes and subpopulations of Brassica napus L.

USDA-ARS?s Scientific Manuscript database

Brassica napus (L.) is a crop of major economic importance that produces canola oil (seed), vegetables, fodder and animal meal. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this s...

Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

PubMed Central

Cheng, Feng; Wu, Jian; Fang, Lu; Sun, Silong; Liu, Bo; Lin, Ke; Bonnema, Guusje; Wang, Xiaowu

2012-01-01

Polyploidization, both ancient and recent, is frequent among plants. A “two-step theory" was proposed to explain the meso-triplication of the Brassica “A" genome: Brassica rapa. By accurately partitioning of this genome, we observed that genes in the less fractioned subgenome (LF) were dominantly expressed over the genes in more fractioned subgenomes (MFs: MF1 and MF2), while the genes in MF1 were slightly dominantly expressed over the genes in MF2. The results indicated that the dominantly expressed genes tended to be resistant against gene fractionation. By re-sequencing two B. rapa accessions: a vegetable turnip (VT117) and a Rapid Cycling line (L144), we found that genes in LF had less non-synonymous or frameshift mutations than genes in MFs; however mutation rates were not significantly different between MF1 and MF2. The differences in gene expression patterns and on-going gene death among the three subgenomes suggest that “two-step" genome triplication and differential subgenome methylation played important roles in the genome evolution of B. rapa. PMID:22567157

Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa.

PubMed

Cheng, Feng; Wu, Jian; Fang, Lu; Sun, Silong; Liu, Bo; Lin, Ke; Bonnema, Guusje; Wang, Xiaowu

2012-01-01

Polyploidization, both ancient and recent, is frequent among plants. A "two-step theory" was proposed to explain the meso-triplication of the Brassica "A" genome: Brassica rapa. By accurately partitioning of this genome, we observed that genes in the less fractioned subgenome (LF) were dominantly expressed over the genes in more fractioned subgenomes (MFs: MF1 and MF2), while the genes in MF1 were slightly dominantly expressed over the genes in MF2. The results indicated that the dominantly expressed genes tended to be resistant against gene fractionation. By re-sequencing two B. rapa accessions: a vegetable turnip (VT117) and a Rapid Cycling line (L144), we found that genes in LF had less non-synonymous or frameshift mutations than genes in MFs; however mutation rates were not significantly different between MF1 and MF2. The differences in gene expression patterns and on-going gene death among the three subgenomes suggest that "two-step" genome triplication and differential subgenome methylation played important roles in the genome evolution of B. rapa.

The Large Subunit rDNA Sequence of Plasmodiophora brassicae Does not Contain Intra-species Polymorphism

PubMed Central

Schwelm, Arne; Berney, Cédric; Dixelius, Christina; Bass, David; Neuhauser, Sigrid

2016-01-01

Clubroot disease caused by Plasmodiophora brassicae is one of the most important diseases of cultivated brassicas. P. brassicae occurs in pathotypes which differ in the aggressiveness towards their Brassica host plants. To date no DNA based method to distinguish these pathotypes has been described. In 2011 polymorphism within the 28S rDNA of P. brassicae was reported which potentially could allow to distinguish pathotypes without the need of time-consuming bioassays. However, isolates of P. brassicae from around the world analysed in this study do not show polymorphism in their LSU rDNA sequences. The previously described polymorphism most likely derived from soil inhabiting Cercozoa more specifically Neoheteromita-like glissomonads. Here we correct the LSU rDNA sequence of P. brassicae. By using FISH we demonstrate that our newly generated sequence belongs to the causal agent of clubroot disease. PMID:27750174

Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

PubMed Central

Branco, Sara; Bi, Ke; Liao, Hui-Ling; Gladieux, Pierre; Badouin, Hélène; Ellison, Christopher E.; Nguyen, Nhu H.; Vilgalys, Rytas; Peay, Kabir G.; Taylor, John W.; Bruns, Thomas D.

2016-01-01

Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation. We found that S. brevipes exhibited overall strong population differentiation, with potential admixture in Canadian populations. This species also displayed genomic signatures of positive selection as well as genomic sites significantly associated with distinct climatic regimes and abiotic environmental parameters. These genomic regions included genes involved in transmembrane transport of substances and helicase activity potentially involved in cold stress response. Our study sheds light on large-scale environmental adaptation in fungi by identifying putative adaptive genes and providing a framework to further investigate the genetic basis of fungal adaptation. PMID:27761941

Feed-forward adaptive-optic correction of a weakly-compressible high-subsonic shear layer

NASA Astrophysics Data System (ADS)

Duffin, Daniel A.

Development of airborne laser systems began in the 1970s with the Airborne Laser Laboratory, a KC135 aircraft with a CO2 laser projected from a beam director mounted atop the aircraft as a hemispherical turret encased in a fairing. It was known that the turbulent air flowing around the turret and separating over the aft portions of the turret would aberrate the laser beam's wavefront (the aero-optic problem); however, the CO2 wavelength, 10.6 mum, was long enough that the aberrating turbulent flow decreased the system's performance by only about 5%. With newer airborne laser systems using wavelengths nearer 1 mum, this same turbulent flow now reduces system performance by more than 95%. It has long been known that if a conjugate waveform is used to pre-distort the outgoing laser's wavefront, the turbulence will actually correct the beam, restoring most of the system's performance. The problem with performing this compensation is that the system for performing this function, the so-called adaptive-optic system, is bandwidth limited in its conventional architecture, by orders of magnitude lower than that required to correct for the aero-optic effects. The research described in this dissertation explored changing the adaptive-optic paradigm from feedback to feed-forward by adding flow control to make the aberration environment predictable rather than unpredictable. This research demonstrated that the turbulent high-speed separated shear layer could be robustly forced into a regularized form. It was also shown that these regularized velocity patterns in the shear layer produced periodic optical aberrations. Extensive measurement and analysis of these convecting aberrations yielded the underlying structure required to produce the conjugate wavefront correction patterns required for a range of laser propagation angles through the shear layer. Ultimately, a feed-forward adaptive-optic system was developed and used to demonstrate the highest-bandwidth correction of aero

Cytological and morphological analysis of hybrids between Brassicoraphanus, and Brassica napus for introgression of clubroot resistant trait into Brassica napus L.

PubMed

Zhan, Zongxiang; Nwafor, Chinedu Charles; Hou, Zhaoke; Gong, Jianfang; Zhu, Bin; Jiang, Yingfen; Zhou, Yongming; Wu, Jiangsheng; Piao, Zhongyun; Tong, Yue; Liu, Chao; Zhang, Chunyu

2017-01-01

Interspecific hybridization is a powerful tool for improvement of crop species, it has the potential to broaden the genetic base and create new plant forms for breeding programs. Synthetic allopolyploid is a widely-used model for the study of genetic recombination and fixed heterosis in Brassica. In Brassica napus breeding, identification and introgression of new sources of clubroot resistance trait from wild or related species into it by hybridization is a long-term crop management strategy for clubroot disease. Radish (Raphanus sativus L.) is a close relative of the Brassica and most radish accessions are immune to the clubroot disease. A synthesized allotetraploid Brassicoraphanus (RRCC, 2n = 36) between R. sativus cv. HQ-04 (2n = 18, RR) and Brassica oleracea var. alboglabra (L.H Bailey) (2n = 18, CC) proved resistant of multiple clubroot disease pathogen P. brassicae. To predict the possibility to transfer the clubroot resistance trait from the RR subgenome of allotetraploid Brassicoraphanus (RRCC, 2n = 36) into Brassica napus (AACC, 2n = 38), we analyzed the frequency of chromosome pairings in the F1 hybrids produced from a cross between B. napus cv. HS5 and the allotetraploid, characterize the genomic composition of some backcrossed progeny (BC1) using GISH, BAC-FISH and AFLP techniques. The level of intergenomic pairing between A and R genomes in the F1 hybrid was high, allosyndetic bivalents formed in 73.53% PMCs indicative of significant level of homeologous recombination between two genomes and high probability of incorporating chromosomal segments/genes from R-genome into A/C-genomes. The BC1 plants inherited variant extra R chromosomes or fragments from allotetraploid as revealed by GISH and AFLP analysis. 13.51% BC2 individuals were resistant to clubroot disease, and several resistance lines had high pollen fertility, Overall, the genetic material presented in this work represents a potential new genetic resource for practical use in breeding B. napus

Floral Initiation in Response to Planting Date Reveals the Key Role of Floral Meristem Differentiation Prior to Budding in Canola (Brassica napus L.).

PubMed

Zhang, Yaofeng; Zhang, Dongqing; Yu, Huasheng; Lin, Baogang; Fu, Ying; Hua, Shuijin

2016-01-01

In Brassica napus, floral development is a decisive factor in silique formation, and it is influenced by many cultivation practices including planting date. However, the effect of planting date on floral initiation in canola is poorly understood at present. A field experiment was conducted using a split plot design, in which three planting dates (early, 15 September, middle, 1 October, and late, 15 October) served as main plot and five varieties differing in maturity (1358, J22, Zhongshuang 11, Zheshuang 8, and Zheyou 50) employed as subplot. The purpose of this study was to shed light on the process of floral meristem (FM) differentiation, the influence of planting date on growth period (GP) and floral initiation, and silique formation. The main stages of FM developments can be divided into four stages: first, the transition from shoot apical meristem to FM; second, flower initiation; third, gynoecium and androecium differentiation; and fourth, bud formation. Our results showed that all genotypes had increased GPs from sowing to FM differentiation as planting date was delayed while the GPs from FM differentiation to budding varied year by year except the very early variety, 1358. Based on the number of flowers present at the different reproductive stages, the flowers produced from FM differentiation to budding closely approximated the final silique even though the FM differentiated continuously after budding and peaked generally at the middle flowering stage. The ratio of siliques to maximum flower number ranged from 48 to 80%. These results suggest that (1) the period from FM differentiation to budding is vital for effective flower and silique formation although there was no significant correlation between the length of the period and effective flowers and siliques, and (2) the increased number of flowers from budding were generally ineffective. Therefore, maximizing flower numbers prior to budding will improve silique numbers, and reducing FM degeneration should

Adaptive Differentiation of Quantitative Traits in the Globally Distributed Weed, Wild Radish (Raphanus raphanistrum)

PubMed Central

Sahli, Heather F.; Conner, Jeffrey K.; Shaw, Frank H.; Howe, Stephen; Lale, Allison

2008-01-01

Weedy species with wide geographical distributions may face strong selection to adapt to new environments, which can lead to adaptive genetic differentiation among populations. However, genetic drift, particularly due to founder effects, will also commonly result in differentiation in colonizing species. To test whether selection has contributed to trait divergence, we compared differentiation at eight microsatellite loci (measured as FST) to differentiation of quantitative floral and phenological traits (measured as QST) of wild radish (Raphanus raphanistrum) across populations from three continents. We sampled eight populations: seven naturalized populations and one from its native range. By comparing estimates of QST and FST, we found that petal size was the only floral trait that may have diverged more than expected due to drift alone, but inflorescence height, flowering time, and rosette formation have greatly diverged between the native and nonnative populations. Our results suggest the loss of a rosette and the evolution of early flowering time may have been the key adaptations enabling wild radish to become a major agricultural weed. Floral adaptation to different pollinators does not seem to have been as necessary for the success of wild radish in new environments. PMID:18854585

Cold acclimation alters DNA methylation patterns and confers tolerance to heat and increases growth rate in Brassica rapa

PubMed Central

Liu, Tongkun; Li, Ying; Duan, Weike; Huang, Feiyi

2017-01-01

Abstract Epigenetic modifications are implicated in plant adaptations to abiotic stresses. Exposure of plants to one stress can induce resistance to other stresses, a process termed cross-adaptation, which is not well understood. In this study, we aimed to unravel the epigenetic basis of elevated heat-tolerance in cold-acclimated Brassica rapa by conducting a genome-wide DNA methylation analysis of leaves from control (CK) and cold-acclimated (CA) plants. We found that both methylation and demethylation occurred during cold acclimation. Two significantly altered pathways, malate dehydrogenase activity and carbon fixation, and 1562 differentially methylated genes, including BramMDH1, BraKAT2, BraSHM4, and Bra4CL2, were identified in CA plants. Genetic validation and treatment of B. rapa with 5-aza-2-deoxycytidine (Aza) suggested that promoter demethylation of four candidate genes increased their transcriptional activities. Physiological analysis suggested that elevated heat-tolerance and high growth rate were closely related to increases in organic acids and photosynthesis, respectively. Functional analyses demonstrated that the candidate gene BramMDH1 (mMDH: mitochondrial malate dehydrogenase) directly enhances organic acids and photosynthesis to increase heat-tolerance and growth rate in Arabidopsis. However, Aza-treated B. rapa, which also has elevated BramMDH1 levels, did not exhibit enhanced heat-tolerance. We therefore suggest that DNA demethylation alone is not sufficient to increase heat-tolerance. This study demonstrates that altered DNA methylation contributes to cross-adaptation. PMID:28158841

Leaf Colour as a Signal of Chemical Defence to Insect Herbivores in Wild Cabbage (Brassica oleracea).

PubMed

Green, Jonathan P; Foster, Rosie; Wilkins, Lucas; Osorio, Daniel; Hartley, Susan E

2015-01-01

Leaf colour has been proposed to signal levels of host defence to insect herbivores, but we lack data on herbivory, leaf colour and levels of defence for wild host populations necessary to test this hypothesis. Such a test requires measurements of leaf spectra as they would be sensed by herbivore visual systems, as well as simultaneous measurements of chemical defences and herbivore responses to leaf colour in natural host-herbivore populations. In a large-scale field survey of wild cabbage (Brassica oleracea) populations, we show that variation in leaf colour and brightness, measured according to herbivore spectral sensitivities, predicts both levels of chemical defences (glucosinolates) and abundance of specialist lepidopteran (Pieris rapae) and hemipteran (Brevicoryne brassicae) herbivores. In subsequent experiments, P. rapae larvae achieved faster growth and greater pupal mass when feeding on plants with bluer leaves, which contained lower levels of aliphatic glucosinolates. Glucosinolate-mediated effects on larval performance may thus contribute to the association between P. rapae herbivory and leaf colour observed in the field. However, preference tests found no evidence that adult butterflies selected host plants based on leaf coloration. In the field, B. brassicae abundance varied with leaf brightness but greenhouse experiments were unable to identify any effects of brightness on aphid preference or performance. Our findings suggest that although leaf colour reflects both levels of host defences and herbivore abundance in the field, the ability of herbivores to respond to colour signals may be limited, even in species where performance is correlated with leaf colour.

Leaf Colour as a Signal of Chemical Defence to Insect Herbivores in Wild Cabbage (Brassica oleracea)

PubMed Central

Wilkins, Lucas; Osorio, Daniel; Hartley, Susan E.

2015-01-01

Leaf colour has been proposed to signal levels of host defence to insect herbivores, but we lack data on herbivory, leaf colour and levels of defence for wild host populations necessary to test this hypothesis. Such a test requires measurements of leaf spectra as they would be sensed by herbivore visual systems, as well as simultaneous measurements of chemical defences and herbivore responses to leaf colour in natural host-herbivore populations. In a large-scale field survey of wild cabbage (Brassica oleracea) populations, we show that variation in leaf colour and brightness, measured according to herbivore spectral sensitivities, predicts both levels of chemical defences (glucosinolates) and abundance of specialist lepidopteran (Pieris rapae) and hemipteran (Brevicoryne brassicae) herbivores. In subsequent experiments, P. rapae larvae achieved faster growth and greater pupal mass when feeding on plants with bluer leaves, which contained lower levels of aliphatic glucosinolates. Glucosinolate-mediated effects on larval performance may thus contribute to the association between P. rapae herbivory and leaf colour observed in the field. However, preference tests found no evidence that adult butterflies selected host plants based on leaf coloration. In the field, B. brassicae abundance varied with leaf brightness but greenhouse experiments were unable to identify any effects of brightness on aphid preference or performance. Our findings suggest that although leaf colour reflects both levels of host defences and herbivore abundance in the field, the ability of herbivores to respond to colour signals may be limited, even in species where performance is correlated with leaf colour. PMID:26353086

Identification and characterization of microRNAs in oilseed rape (Brassica napus) responsive to infection with the pathogenic fungus Verticillium longisporum using Brassica AA (Brassica rapa) and CC (Brassica oleracea) as reference genomes.

PubMed

Shen, Dan; Suhrkamp, Ina; Wang, Yu; Liu, Shenyi; Menkhaus, Jan; Verreet, Joseph-Alexander; Fan, Longjiang; Cai, Daguang

2014-11-01

Verticillium longisporum, a soil-borne pathogenic fungus, causes vascular disease in oilseed rape (Brassica napus). We proposed that plant microRNAs (miRNAs) are involved in the plant-V. longisporum interaction. To identify oilseed rape miRNAs, we deep-sequenced two small RNA libraries made from V. longisporum infected/noninfected roots and employed Brassica rapa and Brassica oleracea genomes as references for miRNA prediction and characterization. We identified 893 B. napus miRNAs representing 360 conserved and 533 novel miRNAs, and mapped 429 and 464 miRNAs to the AA and CC genomes, respectively. Microsynteny analysis with the conserved miRNAs and their flanking protein coding sequences revealed 137 AA-CC genome syntenic miRNA pairs and 61 AA and 42 CC genome-unique miRNAs. Sixty-two miRNAs were responsive to the V. longisporum infection. We present data for specific interactions and simultaneously reciprocal changes in the expression levels of the miRNAs and their targets in the infected roots. We demonstrate that miRNAs are involved in the plant-fungus interaction and that miRNA168-Argonaute 1 (AGO1) expression modulation might act as a key regulatory module in a compatible plant-V. longisporum interaction. Our results suggest that V. longisporum may have evolved a virulence mechanism by interference with plant miRNAs to reprogram plant gene expression and achieve infection. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

PubMed

Colautti, Robert I; Lau, Jennifer A

2015-05-01

Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. © 2015 John Wiley & Sons Ltd.

Differentially Private Histogram Publication For Dynamic Datasets: An Adaptive Sampling Approach

PubMed Central

Li, Haoran; Jiang, Xiaoqian; Xiong, Li; Liu, Jinfei

2016-01-01

Differential privacy has recently become a de facto standard for private statistical data release. Many algorithms have been proposed to generate differentially private histograms or synthetic data. However, most of them focus on “one-time” release of a static dataset and do not adequately address the increasing need of releasing series of dynamic datasets in real time. A straightforward application of existing histogram methods on each snapshot of such dynamic datasets will incur high accumulated error due to the composibility of differential privacy and correlations or overlapping users between the snapshots. In this paper, we address the problem of releasing series of dynamic datasets in real time with differential privacy, using a novel adaptive distance-based sampling approach. Our first method, DSFT, uses a fixed distance threshold and releases a differentially private histogram only when the current snapshot is sufficiently different from the previous one, i.e., with a distance greater than a predefined threshold. Our second method, DSAT, further improves DSFT and uses a dynamic threshold adaptively adjusted by a feedback control mechanism to capture the data dynamics. Extensive experiments on real and synthetic datasets demonstrate that our approach achieves better utility than baseline methods and existing state-of-the-art methods. PMID:26973795

Differential flatness properties and multivariable adaptive control of ovarian system dynamics

NASA Astrophysics Data System (ADS)

Rigatos, Gerasimos

2016-12-01

The ovarian system exhibits nonlinear dynamics which is modeled by a set of coupled nonlinear differential equations. The paper proposes adaptive fuzzy control based on differential flatness theory for the complex dynamics of the ovarian system. It is proven that the dynamic model of the ovarian system, having as state variables the LH and the FSH hormones and their derivatives, is a differentially flat one. This means that all its state variables and its control inputs can be described as differential functions of the flat output. By exploiting differential flatness properties the system's dynamic model is written in the multivariable linear canonical (Brunovsky) form, for which the design of a state feedback controller becomes possible. After this transformation, the new control inputs of the system contain unknown nonlinear parts, which are identified with the use of neurofuzzy approximators. The learning procedure for these estimators is determined by the requirement the first derivative of the closed-loop's Lyapunov function to be a negative one. Moreover, Lyapunov stability analysis shows that H-infinity tracking performance is succeeded for the feedback control loop and this assures improved robustness to the aforementioned model uncertainty as well as to external perturbations. The efficiency of the proposed adaptive fuzzy control scheme is confirmed through simulation experiments.

Applications and challenges of next-generation sequencing in Brassica species.

PubMed

Wei, Lijuan; Xiao, Meili; Hayward, Alice; Fu, Donghui

2013-12-01

Next-generation sequencing (NGS) produces numerous (often millions) short DNA sequence reads, typically varying between 25 and 400 bp in length, at a relatively low cost and in a short time. This revolutionary technology is being increasingly applied in whole-genome, transcriptome, epigenome and small RNA sequencing, molecular marker and gene discovery, comparative and evolutionary genomics, and association studies. The Brassica genus comprises some of the most agro-economically important crops, providing abundant vegetables, condiments, fodder, oil and medicinal products. Many Brassica species have undergone the process of polyploidization, which makes their genomes exceptionally complex and can create difficulties in genomics research. NGS injects new vigor into Brassica research, yet also faces specific challenges in the analysis of complex crop genomes and traits. In this article, we review the advantages and limitations of different NGS technologies and their applications and challenges, using Brassica as an advanced model system for agronomically important, polyploid crops. Specifically, we focus on the use of NGS for genome resequencing, transcriptome sequencing, development of single-nucleotide polymorphism markers, and identification of novel microRNAs and their targets. We present trends and advances in NGS technology in relation to Brassica crop improvement, with wide application for sophisticated genomics research into agronomically important polyploid crops.

Adaptive Failure Compensation for Aircraft Flight Control Using Engine Differentials: Regulation

NASA Technical Reports Server (NTRS)

Yu, Liu; Xidong, Tang; Gang, Tao; Joshi, Suresh M.

2005-01-01

The problem of using engine thrust differentials to compensate for rudder and aileron failures in aircraft flight control is addressed in this paper in a new framework. A nonlinear aircraft model that incorporates engine di erentials in the dynamic equations is employed and linearized to describe the aircraft s longitudinal and lateral motion. In this model two engine thrusts of an aircraft can be adjusted independently so as to provide the control flexibility for rudder or aileron failure compensation. A direct adaptive compensation scheme for asymptotic regulation is developed to handle uncertain actuator failures in the linearized system. A design condition is specified to characterize the system redundancy needed for failure compensation. The adaptive regulation control scheme is applied to the linearized model of a large transport aircraft in which the longitudinal and lateral motions are coupled as the result of using engine thrust differentials. Simulation results are presented to demonstrate the effectiveness of the adaptive compensation scheme.

The Large Subunit rDNA Sequence of Plasmodiophora brassicae Does not Contain Intra-species Polymorphism.

PubMed

Schwelm, Arne; Berney, Cédric; Dixelius, Christina; Bass, David; Neuhauser, Sigrid

2016-12-01

Clubroot disease caused by Plasmodiophora brassicae is one of the most important diseases of cultivated brassicas. P. brassicae occurs in pathotypes which differ in the aggressiveness towards their Brassica host plants. To date no DNA based method to distinguish these pathotypes has been described. In 2011 polymorphism within the 28S rDNA of P. brassicae was reported which potentially could allow to distinguish pathotypes without the need of time-consuming bioassays. However, isolates of P. brassicae from around the world analysed in this study do not show polymorphism in their LSU rDNA sequences. The previously described polymorphism most likely derived from soil inhabiting Cercozoa more specifically Neoheteromita-like glissomonads. Here we correct the LSU rDNA sequence of P. brassicae. By using FISH we demonstrate that our newly generated sequence belongs to the causal agent of clubroot disease. Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.

Regulation of Mammalian Physiology by Interconnected Circadian and Feeding Rhythms

PubMed Central

Atger, Florian; Mauvoisin, Daniel; Weger, Benjamin; Gobet, Cédric; Gachon, Frédéric

2017-01-01

Circadian clocks are endogenous timekeeping systems that adapt in an anticipatory fashion the physiology and behavior of most living organisms. In mammals, the master pacemaker resides in the suprachiasmatic nucleus and entrains peripheral clocks using a wide range of signals that differentially schedule physiology and gene expression in a tissue-specific manner. The peripheral clocks, such as those found in the liver, are particularly sensitive to rhythmic external cues like feeding behavior, which modulate the phase and amplitude of rhythmic gene expression. Consequently, the liver clock temporally tunes the expression of many genes involved in metabolism and physiology. However, the circadian modulation of cellular functions also relies on multiple layers of posttranscriptional and posttranslational regulation. Strikingly, these additional regulatory events may happen independently of any transcriptional oscillations, showing that complex regulatory networks ultimately drive circadian output functions. These rhythmic events also integrate feeding-related cues and adapt various metabolic processes to food availability schedules. The importance of such temporal regulation of metabolism is illustrated by metabolic dysfunctions and diseases resulting from circadian clock disruption or inappropriate feeding patterns. Therefore, the study of circadian clocks and rhythmic feeding behavior should be of interest to further advance our understanding of the prevention and therapy of metabolic diseases. PMID:28337174

Metabolic profiling and biological capacity of Pieris brassicae fed with kale (Brassica oleracea L. var. acephala).

PubMed

Ferreres, Federico; Fernandes, Fátima; Oliveira, Jorge M A; Valentão, Patrícia; Pereira, José A; Andrade, Paula B

2009-06-01

Phenolic and organic acid profiles of aqueous extracts from Pieris brassicae material and the host kale (Brassica oleracea L. var. acephala) leaves were determined by HPLC/UV-DAD/MS(n)-ESI and HPLC-UV, respectively. The identified phenolics included acylated and nonacylated flavonoid glycosides, hydroxycinnamic acyl gentiobiosides, and sulphate phenolics. Kale exhibited the highest content (11g/kg lyophilized extract), while no phenolics were identified in the butterflies or exuviae. Nine different organic acids were characterized in the materials, with kale showing the highest amount (112g/kg lyophilized extract). With the exception of the exuviae extract, the rest were screened for bioactivity. Using spectrophotometric microassays, all exhibited antiradical capacity against DPPH and NO in a concentration-dependent way, whereas only kale and excrement extracts were active against superoxide. All displayed activity on intestinal smooth muscle, albeit with distinct relaxation-contraction profiles. Larvae and butterfly extracts were more efficacious for intestinal relaxation than was kale extract, whereas excrement extract evoked only contractions, thus evidencing their different compositions. Collectively, these results show that P. brassicae sequesters and metabolizes kale's phenolic compounds. Moreover, the extract's bioactivities suggest that they may constitute an interesting source of bioactive compounds whose complex chemical structures preclude either synthesis or isolation.

Population genomic analysis reveals differential evolutionary histories and patterns of diversity across subgenomes and subpopulations of Brassica napus L.

DOE PAGES

Gazave, Elodie; Tassone, Erica E.; Ilut, Daniel C.; ...

2016-04-21

Here, the allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia, and America. We detected strong population structure broadlymore » concordant with growth habit and geography, and identified three major genetic groups: spring (SP), winter Europe (WE), and winter Asia (WA). Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.« less

Population genomic analysis reveals differential evolutionary histories and patterns of diversity across subgenomes and subpopulations of Brassica napus L.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gazave, Elodie; Tassone, Erica E.; Ilut, Daniel C.

Here, the allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia, and America. We detected strong population structure broadlymore » concordant with growth habit and geography, and identified three major genetic groups: spring (SP), winter Europe (WE), and winter Asia (WA). Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.« less

Diverse regulatory factors associate with flowering time and yield responses in winter-type Brassica napus.

PubMed

Schiessl, Sarah; Iniguez-Luy, Federico; Qian, Wei; Snowdon, Rod J

2015-09-29

Flowering time, plant height and seed yield are strongly influenced by climatic and day-length adaptation in crop plants. To investigate these traits under highly diverse field conditions in the important oilseed crop Brassica napus, we performed a genome-wide association study using data from diverse agroecological environments spanning three continents. A total of 158 European winter-type B.napus inbred lines were genotyped with 21,623 unique, single-locus single-nucleotide polymorphism (SNP) markers using the Brassica 60 K-SNP Illumina® Infinium consortium array. Phenotypic associations were calculated in the panel over the years 2010-2012 for flowering time, plant height and seed yield in 5 highly diverse locations in Germany, China and Chile, adding up to 11 diverse environments in total. We identified 101 genome regions associating with the onset of flowering, 69 with plant height, 36 with seed yield and 68 cross-trait regions with potential adaptive value. Within these regions, B.napus orthologs for a number of candidate adaptation genes were detected, including central circadian clock components like CIRCADIAN CLOCK- ASSOCIATED 1 (Bna.CCA1) and the important flowering-time regulators FLOWERING LOCUS T (Bna.FT) and FRUITFUL (Bna.FUL). Gene ontology (GO) enrichment analysis of candidate regions suggested that selection of genes involved in post-transcriptional and epigenetic regulation of flowering time may play a potential role in adaptation of B. napus to highly divergent environments. The classical flowering time regulators Bna.FLC and Bna.CO were not found among the candidate regions, although both show functional variation. Allelic effects were additive for plant height and yield, but not for flowering time. The scarcity of positive minor alleles for yield in this breeding pool points to a lack of diversity for adaptation that could restrict yield gain in the face of environmental change. Our study provides a valuable framework to further improve the

Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea.

PubMed

Bhardwaj, Ankur R; Joshi, Gopal; Kukreja, Bharti; Malik, Vidhi; Arora, Priyanka; Pandey, Ritu; Shukla, Rohit N; Bankar, Kiran G; Katiyar-Agarwal, Surekha; Goel, Shailendra; Jagannath, Arun; Kumar, Amar; Agarwal, Manu

2015-01-21

Brassica juncea var. Varuna is an economically important oilseed crop of family Brassicaceae which is vulnerable to abiotic stresses at specific stages in its life cycle. Till date no attempts have been made to elucidate genome-wide changes in its transcriptome against high temperature or drought stress. To gain global insights into genes, transcription factors and kinases regulated by these stresses and to explore information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de-novo assembly to discover B. juncea transcriptome associated with high temperature and drought stresses. We constructed and sequenced three transcriptome libraries namely Brassica control (BC), Brassica high temperature stress (BHS) and Brassica drought stress (BDS). More than 180 million purity filtered reads were generated which were processed through quality parameters and high quality reads were assembled de-novo using SOAPdenovo assembler. A total of 77750 unique transcripts were identified out of which 69,245 (89%) were annotated with high confidence. We established a subset of 19110 transcripts, which were differentially regulated by either high temperature and/or drought stress. Furthermore, 886 and 2834 transcripts that code for transcription factors and kinases, respectively, were also identified. Many of these were responsive to high temperature, drought or both stresses. Maximum number of up-regulated transcription factors in high temperature and drought stress belonged to heat shock factors (HSFs) and dehydration responsive element-binding (DREB) families, respectively. We also identified 239 metabolic pathways, which were perturbed during high temperature and drought treatments. Analysis of gene ontologies associated with differentially regulated genes forecasted their involvement in diverse biological processes. Our study provides first comprehensive discovery of B. juncea

Different zinc sensitivity of Brassica organs is accompanied by distinct responses in protein nitration level and pattern.

PubMed

Feigl, Gábor; Kolbert, Zsuzsanna; Lehotai, Nóra; Molnár, Árpád; Ördög, Attila; Bordé, Ádám; Laskay, Gábor; Erdei, László

2016-03-01

Zinc is an essential microelement, but its excess exerts toxic effects in plants. Heavy metal stress can alter the metabolism of reactive oxygen (ROS) and nitrogen species (RNS) leading to oxidative and nitrosative damages; although the participation of these processes in Zn toxicity and tolerance is not yet known. Therefore this study aimed to evaluate the zinc tolerance of Brassica organs and the putative correspondence of it with protein nitration as a relevant marker for nitrosative stress. Both examined Brassica species (B. juncea and B. napus) proved to be moderate Zn accumulators; however B. napus accumulated more from this metal in its organs. The zinc-induced damages (growth diminution, altered morphology, necrosis, chlorosis, and the decrease of photosynthetic activity) were slighter in the shoot system of B. napus than in B. juncea. The relative zinc tolerance of B. napus shoot was accompanied by moderate changes of the nitration pattern. In contrast, the root system of B. napus suffered more severe damages (growth reduction, altered morphology, viability loss) and slighter increase in nitration level compared to B. juncea. Based on these, the organs of Brassica species reacted differentially to excess zinc, since in the shoot system modification of the nitration pattern occurred (with newly appeared nitrated protein bands), while in the roots, a general increment in the nitroproteome could be observed (the intensification of the same protein bands being present in the control samples). It can be assumed that the significant alteration of nitration pattern is coupled with enhanced zinc sensitivity of the Brassica shoot system and the general intensification of protein nitration in the roots is attached to relative zinc endurance. Copyright © 2015 Elsevier Inc. All rights reserved.

Toward a clinically useful method of predicting early breast-feeding attrition.

PubMed

Lewallen, Lynne Porter; Dick, Margaret J; Wall, Yolanda; Zickefoose, Kimberly Taylor; Hannah, Susan Hensley; Flowers, Janet; Powell, Wanda

2006-08-01

The overall purpose of this study was to revise and test an instrument to identify, during the early postpartum period, women at risk for early breast-feeding attrition. This study was completed in two phases: the first phase tested a revision of the Breast-Feeding Attrition Prediction Tool (BAPT); the second, a new instrument, the Breast-Feeding Attitude Scale (BrAS), which was adapted from the BAPT. The two phases of this study involved 415 pregnant and postpartum women. Women answered questions either by phone (pregnant women) or in their hospital rooms after delivery (postpartum women). Data were analyzed using t tests and reliability analysis. The BAPT did not predict early breast-feeding attrition; however, the BrAS did differentiate between the attitudes of breast-feeding women and those of formula-feeding women and had adequate reliability. Women at risk for early breast-feeding attrition should be identified early so nursing interventions can be directed toward preventing early unintended weaning. Although the BrAS did not reliably identify women at risk in this sample, it did highlight important differences between breast-feeding and formula-feeding women that can be used in designing preconceptional or prenatal educational assessments and interventions.

Herbivory by a Phloem-feeding insect inhibits floral volatile production.

PubMed

Pareja, Martin; Qvarfordt, Erika; Webster, Ben; Mayon, Patrick; Pickett, John; Birkett, Michael; Glinwood, Robert

2012-01-01

There is extensive knowledge on the effects of insect herbivory on volatile emission from vegetative tissue, but little is known about its impact on floral volatiles. We show that herbivory by phloem-feeding aphids inhibits floral volatile emission in white mustard Sinapis alba measured by gas chromatographic analysis of headspace volatiles. The effect of the Brassica specialist aphid Lipaphis erysimi was stronger than the generalist aphid Myzus persicae and feeding by chewing larvae of the moth Plutella xylostella caused no reduction in floral volatile emission. Field observations showed no effect of L. erysimi-mediated floral volatile emission on the total number of flower visits by pollinators. Olfactory bioassays suggested that although two aphid natural enemies could detect aphid inhibition of floral volatiles, their olfactory orientation to infested plants was not disrupted. This is the first demonstration that phloem-feeding herbivory can affect floral volatile emission, and that the outcome of interaction between herbivory and floral chemistry may differ depending on the herbivore's feeding mode and degree of specialisation. The findings provide new insights into interactions between insect herbivores and plant chemistry.

Screening of a Brassica napus bacterial artificial chromosome library using highly parallel single nucleotide polymorphism assays

PubMed Central

2013-01-01

Background Efficient screening of bacterial artificial chromosome (BAC) libraries with polymerase chain reaction (PCR)-based markers is feasible provided that a multidimensional pooling strategy is implemented. Single nucleotide polymorphisms (SNPs) can be screened in multiplexed format, therefore this marker type lends itself particularly well for medium- to high-throughput applications. Combining the power of multiplex-PCR assays with a multidimensional pooling system may prove to be especially challenging in a polyploid genome. In polyploid genomes two classes of SNPs need to be distinguished, polymorphisms between accessions (intragenomic SNPs) and those differentiating between homoeologous genomes (intergenomic SNPs). We have assessed whether the highly parallel Illumina GoldenGate® Genotyping Assay is suitable for the screening of a BAC library of the polyploid Brassica napus genome. Results A multidimensional screening platform was developed for a Brassica napus BAC library which is composed of almost 83,000 clones. Intragenomic and intergenomic SNPs were included in Illumina’s GoldenGate® Genotyping Assay and both SNP classes were used successfully for screening of the multidimensional BAC pools of the Brassica napus library. An optimized scoring method is proposed which is especially valuable for SNP calling of intergenomic SNPs. Validation of the genotyping results by independent methods revealed a success of approximately 80% for the multiplex PCR-based screening regardless of whether intra- or intergenomic SNPs were evaluated. Conclusions Illumina’s GoldenGate® Genotyping Assay can be efficiently used for screening of multidimensional Brassica napus BAC pools. SNP calling was specifically tailored for the evaluation of BAC pool screening data. The developed scoring method can be implemented independently of plant reference samples. It is demonstrated that intergenomic SNPs represent a powerful tool for BAC library screening of a polyploid genome

Comparative mapping of quantitative trait loci sculpting the curd of Brassica oleracea.

PubMed

Lan, T H; Paterson, A H

2000-08-01

The enlarged inflorescence (curd) of cauliflower and broccoli provide not only a popular vegetable for human consumption, but also a unique opportunity for scientists who seek to understand the genetic basis of plant growth and development. By the comparison of quantitative trait loci (QTL) maps constructed from three different F(2) populations, we identified a total of 86 QTL that control eight curd-related traits in Brassica oleracea. The 86 QTL may reflect allelic variation in as few as 67 different genetic loci and 54 ancestral genes. Although the locations of QTL affecting a trait occasionally corresponded between different populations or between different homeologous Brassica chromosomes, our data supported other molecular and morphological data in suggesting that the Brassica genus is rapidly evolving. Comparative data enabled us to identify a number of candidate genes from Arabidopsis that warrant further investigation to determine if some of them might account for Brassica QTL. The Arabidopsis/Brassica system is an important example of both the challenges and opportunities associated with extrapolation of genomic information from facile models to large-genome taxa including major crops.

Impact of selenium supply on se-methylselenocysteine and glucosinolates accumulation in selenium-biofortified brassica sprouts

USDA-ARS?s Scientific Manuscript database

Brassica sprouts are widely marketed as functional foods. Here we examined the effects of Se treatment on the accumulation of anticancer compound Se-methylselenocysteine (SeMSCys) and glucosinolates in Brassica sprouts. Cultivars from the six most extensively consumed Brassica vegetables (broccoli, ...

Large-scale adaptive differentiation in the alpine perennial herb Arabis alpina.

PubMed

Toräng, Per; Wunder, Jörg; Obeso, José Ramón; Herzog, Michel; Coupland, George; Ågren, Jon

2015-04-01

Information about the incidence and magnitude of local adaptation can help to predict the response of natural populations to a changing environment, and should be of particular interest in arctic and alpine environments where the effects of climate change are expected to be severe. To quantify adaptive differentiation in the arctic-alpine perennial herb Arabis alpina, we conducted reciprocal transplant experiments for 3 yr between Spanish and Scandinavian populations. At the sites of one Spanish and one Scandinavian population, we planted seedlings representing two Spanish and four Scandinavian populations, and recorded survival, flowering propensity and fecundity. The experiment was replicated in two subsequent years. The results demonstrate strong adaptive differentiation between A. alpina populations from the two regions. At the field site in Spain, survival and fruit production of Spanish populations were higher than those of Scandinavian populations, while the opposite was true at the site in Scandinavia, and these differences were consistent across years. By comparison, fitness varied little among populations from the same region. The results suggest that the magnitude and geographical scale of local adaptation need to be considered in predictions of the effects of global change on the dynamics of arctic and alpine plant populations. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

PubMed Central

2014-01-01

Background Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus. Results We generate an assembly representing 75% of the predicted B. oleracea genome using a hybrid Illumina/Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of B. oleracea compared to its close relative B. rapa. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event. Conclusions Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes. PMID:24916971

Adaptive group coordination and role differentiation.

PubMed

Roberts, Michael E; Goldstone, Robert L

2011-01-01

Many real world situations (potluck dinners, academic departments, sports teams, corporate divisions, committees, seminar classes, etc.) involve actors adjusting their contributions in order to achieve a mutually satisfactory group goal, a win-win result. However, the majority of human group research has involved situations where groups perform poorly because task constraints promote either individual maximization behavior or diffusion of responsibility, and even successful tasks generally involve the propagation of one correct solution through a group. Here we introduce a group task that requires complementary actions among participants in order to reach a shared goal. Without communication, group members submit numbers in an attempt to collectively sum to a randomly selected target number. After receiving group feedback, members adjust their submitted numbers until the target number is reached. For all groups, performance improves with task experience, and group reactivity decreases over rounds. Our empirical results provide evidence for adaptive coordination in human groups, and as the coordination costs increase with group size, large groups adapt through spontaneous role differentiation and self-consistency among members. We suggest several agent-based models with different rules for agent reactions, and we show that the empirical results are best fit by a flexible, adaptive agent strategy in which agents decrease their reactions when the group feedback changes. The task offers a simple experimental platform for studying the general problem of group coordination while maximizing group returns, and we distinguish the task from several games in behavioral game theory.

Brassica greens herbicide screening

USDA-ARS?s Scientific Manuscript database

The objective of this study was to screen herbicides for potential use in brassica greens. Plots were in a RBD with 4 replications. The study was direct seeded on May 19, 2009 with a seeding rate of 272,000 seeds/acre (‘Savanna’ mustard). Treatments included trifluralin PPI + DCPA pre-emergence ap...

Continuous Adaptive Population Reduction (CAPR) for Differential Evolution Optimization.

PubMed

Wong, Ieong; Liu, Wenjia; Ho, Chih-Ming; Ding, Xianting

2017-06-01

Differential evolution (DE) has been applied extensively in drug combination optimization studies in the past decade. It allows for identification of desired drug combinations with minimal experimental effort. This article proposes an adaptive population-sizing method for the DE algorithm. Our new method presents improvements in terms of efficiency and convergence over the original DE algorithm and constant stepwise population reduction-based DE algorithm, which would lead to a reduced number of cells and animals required to identify an optimal drug combination. The method continuously adjusts the reduction of the population size in accordance with the stage of the optimization process. Our adaptive scheme limits the population reduction to occur only at the exploitation stage. We believe that continuously adjusting for a more effective population size during the evolutionary process is the major reason for the significant improvement in the convergence speed of the DE algorithm. The performance of the method is evaluated through a set of unimodal and multimodal benchmark functions. In combining with self-adaptive schemes for mutation and crossover constants, this adaptive population reduction method can help shed light on the future direction of a completely parameter tune-free self-adaptive DE algorithm.

The use of solution adaptive grids in solving partial differential equations

NASA Technical Reports Server (NTRS)

Anderson, D. A.; Rai, M. M.

1982-01-01

The grid point distribution used in solving a partial differential equation using a numerical method has a substantial influence on the quality of the solution. An adaptive grid which adjusts as the solution changes provides the best results when the number of grid points available for use during the calculation is fixed. Basic concepts used in generating and applying adaptive grids are reviewed in this paper, and examples illustrating applications of these concepts are presented.

Differential profiles of direct and indirect modification of vector feeding behaviour by a plant virus.

PubMed

He, Wen-Bo; Li, Jie; Liu, Shu-Sheng

2015-01-08

Plant viruses interact with their insect vectors directly and indirectly via host plants, and this tripartite interaction may produce fitness benefits to both the vectors and the viruses. Our previous studies show that the Middle East-Asia Minor 1 (MEAM1) species of the whitefly Bemisia tabaci complex improved its performance on tobacco plants infected by the Tomato yellow leaf curl China virus (TYLCCNV), which it transmits, although virus infection of the whitefly per se reduced its performance. Here, we use electrical penetration graph recording to investigate the direct and indirect effects of TYLCCNV on the feeding behaviour of MEAM1. When feeding on either cotton, a non-host of TYLCCNV, or uninfected tobacco, a host of TYLCCNV, virus-infection of the whiteflies impeded their feeding. Interestingly, when viruliferous whiteflies fed on virus-infected tobacco, their feeding activities were no longer negatively affected; instead, the virus promoted whitefly behaviour related to rapid and effective sap ingestion. Our findings show differential profiles of direct and indirect modification of vector feeding behaviour by a plant virus, and help to unravel the behavioural mechanisms underlying a mutualistic relationship between an insect vector and a plant virus that also has features reminiscent of an insect pathogen.

Differential profiles of direct and indirect modification of vector feeding behaviour by a plant virus

PubMed Central

He, Wen-Bo; Li, Jie; Liu, Shu-Sheng

2015-01-01

Plant viruses interact with their insect vectors directly and indirectly via host plants, and this tripartite interaction may produce fitness benefits to both the vectors and the viruses. Our previous studies show that the Middle East-Asia Minor 1 (MEAM1) species of the whitefly Bemisia tabaci complex improved its performance on tobacco plants infected by the Tomato yellow leaf curl China virus (TYLCCNV), which it transmits, although virus infection of the whitefly per se reduced its performance. Here, we use electrical penetration graph recording to investigate the direct and indirect effects of TYLCCNV on the feeding behaviour of MEAM1. When feeding on either cotton, a non-host of TYLCCNV, or uninfected tobacco, a host of TYLCCNV, virus-infection of the whiteflies impeded their feeding. Interestingly, when viruliferous whiteflies fed on virus-infected tobacco, their feeding activities were no longer negatively affected; instead, the virus promoted whitefly behaviour related to rapid and effective sap ingestion. Our findings show differential profiles of direct and indirect modification of vector feeding behaviour by a plant virus, and help to unravel the behavioural mechanisms underlying a mutualistic relationship between an insect vector and a plant virus that also has features reminiscent of an insect pathogen. PMID:25567524

Harnessing the Power of Cruciferous Vegetables: Developing a Biomarker for Brassica Vegetable Consumption Using Urinary 3,3'-Diindolylmethane.

PubMed

Fujioka, Naomi; Ransom, Benjamin W; Carmella, Steven G; Upadhyaya, Pramod; Lindgren, Bruce R; Roper-Batker, Astia; Hatsukami, Dorothy K; Fritz, Vincent A; Rohwer, Charles; Hecht, Stephen S

2016-10-01

Glucobrassicin in Brassica vegetables gives rise to indole-3-carbinol (I3C), a compound with potent anticancer effects in preclinical models. We previously showed that the urinary metabolite 3,3'-diindolylmethane (DIM) could discriminate between volunteers fed high and low doses of Brassica vegetables. However, the quantitative relationship between glucobrassicin exposure and urinary DIM level is unclear. We conducted a clinical trial to examine the hypotheses that a range of glucobrassicin exposure from Brassica vegetables is reflected in urinary DIM and that this effect plateaus. Forty-five subjects consumed vegetables, a mixture of brussels sprouts and/or cabbage, at one of seven discrete dose levels of glucobrassicin ranging from 25 to 500 μmol, once daily for 2 consecutive days. All urine was collected for 24 hours after each vegetable-eating session. Urinary DIM was measured using our published liquid chromatography-electrospray ionization-tandem mass spectrometry-selected reaction monitoring (LC/ESI-MS/MS-SRM) method. Urinary DIM excretion increased predictably with increasing glucobrassicin dose and plateaued between 200 and 300 μmol of glucobrassicin. The association between glucobrassicin dose and urinary DIM was strong and positive (R 2 = 0.68). The majority of DIM was excreted in the first 12 hours after vegetable consumption. We conclude that urinary DIM is a reliable biomarker of glucobrassicin exposure and I3C uptake and that feeding glucobrassicin beyond 200 μmol did not consistently lead to more urinary DIM, suggesting a plateau in potential chemopreventive benefit. Cancer Prev Res; 9(10); 788-93. ©2016 AACR. ©2016 American Association for Cancer Research.

Cephalopods as Predators: A Short Journey among Behavioral Flexibilities, Adaptions, and Feeding Habits

PubMed Central

Villanueva, Roger; Perricone, Valentina; Fiorito, Graziano

2017-01-01

The diversity of cephalopod species and the differences in morphology and the habitats in which they live, illustrates the ability of this class of molluscs to adapt to all marine environments, demonstrating a wide spectrum of patterns to search, detect, select, capture, handle, and kill prey. Photo-, mechano-, and chemoreceptors provide tools for the acquisition of information about their potential preys. The use of vision to detect prey and high attack speed seem to be a predominant pattern in cephalopod species distributed in the photic zone, whereas in the deep-sea, the development of mechanoreceptor structures and the presence of long and filamentous arms are more abundant. Ambushing, luring, stalking and pursuit, speculative hunting and hunting in disguise, among others are known modes of hunting in cephalopods. Cannibalism and scavenger behavior is also known for some species and the development of current culture techniques offer evidence of their ability to feed on inert and artificial foods. Feeding requirements and prey choice change throughout development and in some species, strong ontogenetic changes in body form seem associated with changes in their diet and feeding strategies, although this is poorly understood in planktonic and larval stages. Feeding behavior is altered during senescence and particularly in brooding octopus females. Cephalopods are able to feed from a variety of food sources, from detritus to birds. Their particular requirements of lipids and copper may help to explain why marine crustaceans, rich in these components, are common prey in all cephalopod diets. The expected variation in climate change and ocean acidification and their effects on chemoreception and prey detection capacities in cephalopods are unknown and needs future research. PMID:28861006

Genome resequencing and comparative variome analysis in a Brassica rapa and Brassica oleracea collection.

PubMed

Cheng, Feng; Wu, Jian; Cai, Chengcheng; Fu, Lixia; Liang, Jianli; Borm, Theo; Zhuang, Mu; Zhang, Yangyong; Zhang, Fenglan; Bonnema, Guusje; Wang, Xiaowu

2016-12-20

The closely related species Brassica rapa and B. oleracea encompass a wide range of vegetable, fodder and oil crops. The release of their reference genomes has facilitated resequencing collections of B. rapa and B. oleracea aiming to build their variome datasets. These data can be used to investigate the evolutionary relationships between and within the different species and the domestication of the crops, hereafter named morphotypes. These data can also be used in genetic studies aiming at the identification of genes that influence agronomic traits. We selected and resequenced 199 B. rapa and 119 B. oleracea accessions representing 12 and nine morphotypes, respectively. Based on these resequencing data, we obtained 2,249,473 and 3,852,169 high quality SNPs (single-nucleotide polymorphisms), as well as 303,617 and 417,004 InDels for the B. rapa and B. oleracea populations, respectively. The variome datasets of B. rapa and B. oleracea represent valuable resources to researchers working on evolution, domestication or breeding of Brassica vegetable crops.

Functional alleles of the flowering time regulator FRIGIDA in the Brassica oleracea genome

PubMed Central

2012-01-01

Background Plants adopt different reproductive strategies as an adaptation to growth in a range of climates. In Arabidopsis thaliana FRIGIDA (FRI) confers a vernalization requirement and thus winter annual habit by increasing the expression of the MADS box transcriptional repressor FLOWERING LOCUS C (FLC). Variation at FRI plays a major role in A. thaliana life history strategy, as independent loss-of-function alleles that result in a rapid-cycling habit in different accessions, appear to have evolved many times. The aim of this study was to identify and characterize orthologues of FRI in Brassica oleracea. Results We describe the characterization of FRI from Brassica oleracea and identify the two B. oleracea FRI orthologues (BolC.FRI.a and BolC.FRI.b). These show extensive amino acid conservation in the central and C-terminal regions to FRI from other Brassicaceae, including A. thaliana, but have a diverged N-terminus. The genes map to two of the three regions of B. oleracea chromosomes syntenic to part of A. thaliana chromosome 5 suggesting that one of the FRI copies has been lost since the ancient triplication event that formed the B. oleracea genome. This genomic position is not syntenic with FRI in A. thaliana and comparative analysis revealed a recombination event within the A. thaliana FRI promoter. This relocated A. thaliana FRI to chromosome 4, very close to the nucleolar organizer region, leaving a fragment of FRI in the syntenic location on A. thaliana chromosome 5. Our data show this rearrangement occurred after the divergence from A. lyrata. We explored the allelic variation at BolC.FRI.a within cultivated B. oleracea germplasm and identified two major alleles, which appear equally functional both to each other and A. thaliana FRI, when expressed as fusions in A. thaliana. Conclusions We identify the two Brassica oleracea FRI genes, one of which we show through A. thaliana complementation experiments is functional, and show their genomic location is

Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica.

PubMed

Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J S

2015-12-01

Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

Differential protein expression during colonic adaptation in ultra-short bowel rats

PubMed Central

Jiang, Hai-Ping; Chen, Tao; Yan, Guang-Rong; Chen, Dan

2011-01-01

AIM: To investigate the proteins involved in colonic adaptation and molecular mechanisms of colonic adaptation in rats with ultra-short bowel syndrome (USBS). METHODS: Sprague Dawley rats were randomly assigned to three groups: USBS group (10 rats) undergoing an approximately 90%-95% small bowel resection; sham-operation group (10 rats) undergoing small bowel transaction and anastomosis; and control group (ten normal rats). Colon morphology and differential protein expression was analyzed after rats were given post-surgical enteral nutrition for 21 d. Protein expression in the colonic mucosa was analyzed by two-dimensional electrophoresis (2-DE) in all groups. Differential protein spots were detected by ImageMaster 2D Platinum software and were further analyzed with matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight-mass spectrometric (MALDI-TOF/TOF-MS) analysis. RESULTS: The colonic mucosal thickness significantly increased in the USBS group compared with the control group (302.1 ± 16.9 μm vs 273.7 ± 16.0 μm, P < 0.05). There was no statistically significant difference between the sham-operation group and control group (P > 0.05). The height of colon plica markedly improved in USBS group compared with the control group (998.4 ± 81.2 μm vs 883.4 ± 39.0 μm, P < 0.05). There was no statistically significant difference between the sham-operation and control groups (P > 0.05). A total of 141 differential protein spots were found in the USBS group. Forty-nine of these spots were down-regulated while 92 protein spots were up-regulated by over 2-folds. There were 133 differential protein spots in USBS group. Thirty of these spots were down-regulated and 103 were up-regulated. There were 47 common differential protein spots among the three groups, including 17 down-regulated protein spots and 30 up-regulated spots. Among 47 differential spots, eight up-regulated proteins were identified by MALDI-TOF/TOF-MS. These proteins were previously

Differential protein expression during colonic adaptation in ultra-short bowel rats.

PubMed

Jiang, Hai-Ping; Chen, Tao; Yan, Guang-Rong; Chen, Dan

2011-05-28

To investigate the proteins involved in colonic adaptation and molecular mechanisms of colonic adaptation in rats with ultra-short bowel syndrome (USBS). Sprague Dawley rats were randomly assigned to three groups: USBS group (10 rats) undergoing an approximately 90%-95% small bowel resection; sham-operation group (10 rats) undergoing small bowel transaction and anastomosis; and control group (ten normal rats). Colon morphology and differential protein expression was analyzed after rats were given post-surgical enteral nutrition for 21 d. Protein expression in the colonic mucosa was analyzed by two-dimensional electrophoresis (2-DE) in all groups. Differential protein spots were detected by ImageMaster 2D Platinum software and were further analyzed with matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight-mass spectrometric (MALDI-TOF/TOF-MS) analysis. The colonic mucosal thickness significantly increased in the USBS group compared with the control group (302.1 ± 16.9 μm vs 273.7 ± 16.0 μm, P < 0.05). There was no statistically significant difference between the sham-operation group and control group (P > 0.05). The height of colon plica markedly improved in USBS group compared with the control group (998.4 ± 81.2 μm vs 883.4 ± 39.0 μm, P < 0.05). There was no statistically significant difference between the sham-operation and control groups (P > 0.05). A total of 141 differential protein spots were found in the USBS group. Forty-nine of these spots were down-regulated while 92 protein spots were up-regulated by over 2-folds. There were 133 differential protein spots in USBS group. Thirty of these spots were down-regulated and 103 were up-regulated. There were 47 common differential protein spots among the three groups, including 17 down-regulated protein spots and 30 up-regulated spots. Among 47 differential spots, eight up-regulated proteins were identified by MALDI-TOF/TOF-MS. These proteins were previously reported to be involved in

A Self Adaptive Differential Evolution Algorithm for Global Optimization

NASA Astrophysics Data System (ADS)

Kumar, Pravesh; Pant, Millie

This paper presents a new Differential Evolution algorithm based on hybridization of adaptive control parameters and trigonometric mutation. First we propose a self adaptive DE named ADE where choice of control parameter F and Cr is not fixed at some constant value but is taken iteratively. The proposed algorithm is further modified by applying trigonometric mutation in it and the corresponding algorithm is named as ATDE. The performance of ATDE is evaluated on the set of 8 benchmark functions and the results are compared with the classical DE algorithm in terms of average fitness function value, number of function evaluations, convergence time and success rate. The numerical result shows the competence of the proposed algorithm.

Adaptive Failure Compensation for Aircraft Tracking Control Using Engine Differential Based Model

NASA Technical Reports Server (NTRS)

Liu, Yu; Tang, Xidong; Tao, Gang; Joshi, Suresh M.

2006-01-01

An aircraft model that incorporates independently adjustable engine throttles and ailerons is employed to develop an adaptive control scheme in the presence of actuator failures. This model captures the key features of aircraft flight dynamics when in the engine differential mode. Based on this model an adaptive feedback control scheme for asymptotic state tracking is developed and applied to a transport aircraft model in the presence of two types of failures during operation, rudder failure and aileron failure. Simulation results are presented to demonstrate the adaptive failure compensation scheme.

Development and molecular-genetic characterization of a stable Brassica allohexaploid.

PubMed

Gupta, Mehak; Atri, Chhaya; Agarwal, Neha; Banga, Surinder Singh

2016-11-01

We report first-time synthesis of a stable Brassica allohexaploid. It may evolve into a new species and also advance our understanding of pairing regulation and genome evolution in complex allopolyploids. Crop Brassicas include both monogenomic and digenomic species. A trigenomic Brassica (AABBCC) is not known to exist in nature. Past attempts to synthesize a stable allohexaploid were not successful due to aberrant meiosis and very high proportion of aneuploid plants in the selfed progenies. We report the development of a stable allohexaploid Brassica (2n = 54; AABBCC). Genomic in situ hybridization confirmed the complete assemblage of three genomes. Only allohexaploids involving B. rapa cv. R01 (2n = 20; AA) as pollinator with a set of B. carinata (2n = 34; BBCC) were stable. These exhibited a high proportion (0.78-0.94) of pollen mother cells with normal meiosis and an excellent hexaploid ratio (0.80-0.94) in the selfed progenies. Stability of two allohexaploid combinations was demonstrated from H 1 to H 4 generations at two very diverse locations in India. Graphical genotyping of allohexaploids allowed detection of chromosome fragment exchanges among three genomes. These were much smaller for meiotically stable allohexaploids as compared to unstable ones. The putative hexaploids were morphologically closer to the female donor, B. carinata, for leaf morphology, inflorescence structure and flower shape. The newly formed allohexaploid may also provide unique opportunities to investigate the immediate genetic and genomic consequences of a Brassica allohexaploid with three resident genomes.

Development of a NIRS method to measure quality characteristics in Brassica germplasm

USDA-ARS?s Scientific Manuscript database

Hydrotreated renewable jet (HRJ) fuels from plant oils have been commercially demonstrated as an alternative to petroleum jet fuels, but full scale production has not occurred because of concerns over cost and competition with food production. Rapeseed (Brassica napus), along with Brassica carinata,...

Mechanism of Salt-Induced Self-Compatibility Dissected by Comparative Proteomic Analysis in Brassica napus L.

PubMed

Yang, Yong; Liu, Zhiquan; Zhang, Tong; Zhou, Guilong; Duan, Zhiqiang; Li, Bing; Dou, Shengwei; Liang, Xiaomei; Tu, Jinxing; Shen, Jinxiong; Yi, Bin; Fu, Tingdong; Dai, Cheng; Ma, Chaozhi

2018-06-03

Self-incompatibility (SI) in plants genetically prevents self-fertilization to promote outcrossing and genetic diversity. Its hybrids in Brassica have been widely cultivated due to the propagation of SI lines by spraying a salt solution. We demonstrated that suppression of Brassica napus SI from edible salt solution treatment was ascribed to sodium chloride and independent of S haplotypes, but it did not obviously change the expression of SI - related genes. Using the isobaric tags for relative and absolute quantitation (iTRAQ) technique, we identified 885 differentially accumulated proteins (DAPs) in Brassica napus stigmas of un-pollinated (UP), pollinated with compatible pollen (PC), pollinated with incompatible pollen (PI), and pollinated with incompatible pollen after edible salt solution treatment (NA). Of the 307 DAPs in NA/UP, 134 were unique and 94 were shared only with PC/UP. In PC and NA, some salt stress protein species, such as glyoxalase I , were induced, and these protein species were likely to participate in the self-compatibility (SC) pathway. Most of the identified protein species were related to metabolic pathways, biosynthesis of secondary metabolites, ribosome, and so on. A systematic analysis implied that salt treatment-overcoming SI in B. napus was likely conferred by at least five different physiological mechanisms: (i) the use of Ca 2+ as signal molecule; (ii) loosening of the cell wall to allow pollen tube penetration; (iii) synthesis of compatibility factor protein species for pollen tube growth; (iv) depolymerization of microtubule networks to facilitate pollen tube movement; and (v) inhibition of protein degradation pathways to restrain the SI response.

Current Status and Challenges in Identifying Disease Resistance Genes in Brassica napus

PubMed Central

Neik, Ting Xiang; Barbetti, Martin J.; Batley, Jacqueline

2017-01-01

Brassica napus is an economically important crop across different continents including temperate and subtropical regions in Europe, Canada, South Asia, China and Australia. Its widespread cultivation also brings setbacks as it plays host to fungal, oomycete and chytrid pathogens that can lead to serious yield loss. For sustainable crop production, identification of resistance (R) genes in B. napus has become of critical importance. In this review, we discuss four key pathogens affecting Brassica crops: Clubroot (Plasmodiophora brassicae), Blackleg (Leptosphaeria maculans and L. biglobosa), Sclerotinia Stem Rot (Sclerotinia sclerotiorum), and Downy Mildew (Hyaloperonospora parasitica). We first review current studies covering prevalence of these pathogens on Brassica crops and highlight the R genes and QTL that have been identified from Brassica species against these pathogens. Insights into the relationships between the pathogen and its Brassica host, the unique host resistance mechanisms and how these affect resistance outcomes is also presented. We discuss challenges in identification and deployment of R genes in B. napus in relation to highly specific genetic interactions between host subpopulations and pathogen pathotypes and emphasize the need for common or shared techniques and research materials or tighter collaboration between researchers to reconcile the inconsistencies in the research outcomes. Using current genomics tools, we provide examples of how characterization and cloning of R genes in B. napus can be carried out more effectively. Lastly, we put forward strategies to breed resistant cultivars through introgressions supported by genomic approaches and suggest prospects that can be implemented in the future for a better, pathogen-resistant B. napus. PMID:29163558

Management of Rhizoctonia Damping-off of Brassica Oilseed Crops in the PNW

USDA-ARS?s Scientific Manuscript database

Rhizoctonia solani can cause pre and post-emergence damping off of Brassica oilseed species with adverse effects on stand establishment. In greenhouse experiments, we have examined resistance to two groups (AGs) of Rhizoctonia solani among various Brassica species and varieties. R. solani AG 2-1 is ...

Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides.

PubMed

Ren, Jing; Chen, Liang; Jin, Xiaoli; Zhang, Miaomiao; You, Frank M; Wang, Jirui; Frenkel, Vladimir; Yin, Xuegui; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

2017-01-01

Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ F ST ≤ 0.15) or high genetic differentiation ( F ST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different F ST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.

Differentials in colostrum feeding among lactating women of block RS Pura of J and K: A lesson for nursing practice.

PubMed

Raina, Sunil Kumar; Mengi, Vijay; Singh, Gurdeep

2012-07-01

Breast feeding is universally and traditionally practicised in India. Experts advocate breast feeding as the best method of feeding young infants. To assess the role of various factors in determining colostrum feeding in block R. S. Pura of district Jammu. A stratified two-stage design with villages as the primary sampling unit and lactating mothers as secondary sampling unit. Villages were divided into different clusters on the basis of population and sampling units were selected by a simple random technique. Breastfeeding is almost universal in R. S. Pura. Differentials in discarding the first milk were not found to be important among various socioeconomic groups and the phenomenon appeared more general than specific.

Quantification of Plasmodiophora brassicae Using a DNA-Based Soil Test Facilitates Sustainable Oilseed Rape Production

PubMed Central

Wallenhammar, Ann-Charlotte; Gunnarson, Albin; Hansson, Fredrik; Jonsson, Anders

2016-01-01

Outbreaks of clubroot disease caused by the soil-borne obligate parasite Plasmodiophora brassicae are common in oilseed rape (OSR) in Sweden. A DNA-based soil testing service that identifies fields where P. brassicae poses a significant risk of clubroot infection is now commercially available. It was applied here in field surveys to monitor the prevalence of P. brassicae DNA in field soils intended for winter OSR production and winter OSR field experiments. In 2013 in Scania, prior to planting, P. brassicae DNA was detected in 60% of 45 fields on 10 of 18 farms. In 2014, P. brassicae DNA was detected in 44% of 59 fields in 14 of 36 farms, in the main winter OSR producing region in southern Sweden. P. brassicae was present indicative of a risk for >10% yield loss with susceptible cultivars (>1300 DNA copies g soil−1) in 47% and 44% of fields in 2013 and 2014 respectively. Furthermore, P. brassicae DNA was indicative of sites at risk of complete crop failure if susceptible cultivars were grown (>50 000 copies g−1 soil) in 14% and 8% of fields in 2013 and 2014, respectively. A survey of all fields at Lanna research station in western Sweden showed that P. brassicae was spread throughout the farm, as only three of the fields (20%) showed infection levels below the detection limit for P.brassicae DNA, while the level was >50,000 DNA copies g−1 soil in 20% of the fields. Soil-borne spread is of critical importance and soil scraped off footwear showed levels of up to 682 million spores g−1 soil. Soil testing is an important tool for determining the presence of P. brassicae and providing an indication of potential yield loss, e.g., in advisory work on planning for a sustainable OSR crop rotation. This soil test is gaining acceptance as a tool that increases the likelihood of success in precision agriculture and in applied research conducted in commercial oilseed fields and at research stations. The present application highlights the importance of prevention of

Quantification of Plasmodiophora brassicae Using a DNA-Based Soil Test Facilitates Sustainable Oilseed Rape Production.

PubMed

Wallenhammar, Ann-Charlotte; Gunnarson, Albin; Hansson, Fredrik; Jonsson, Anders

2016-04-22

Outbreaks of clubroot disease caused by the soil-borne obligate parasite Plasmodiophora brassicae are common in oilseed rape (OSR) in Sweden. A DNA-based soil testing service that identifies fields where P. brassicae poses a significant risk of clubroot infection is now commercially available. It was applied here in field surveys to monitor the prevalence of P. brassicae DNA in field soils intended for winter OSR production and winter OSR field experiments. In 2013 in Scania, prior to planting, P. brassicae DNA was detected in 60% of 45 fields on 10 of 18 farms. In 2014, P. brassicae DNA was detected in 44% of 59 fields in 14 of 36 farms, in the main winter OSR producing region in southern Sweden. P. brassicae was present indicative of a risk for >10% yield loss with susceptible cultivars (>1300 DNA copies g soil(-1)) in 47% and 44% of fields in 2013 and 2014 respectively. Furthermore, P. brassicae DNA was indicative of sites at risk of complete crop failure if susceptible cultivars were grown (>50 000 copies g(-1) soil) in 14% and 8% of fields in 2013 and 2014, respectively. A survey of all fields at Lanna research station in western Sweden showed that P. brassicae was spread throughout the farm, as only three of the fields (20%) showed infection levels below the detection limit for P.brassicae DNA, while the level was >50,000 DNA copies g(-1) soil in 20% of the fields. Soil-borne spread is of critical importance and soil scraped off footwear showed levels of up to 682 million spores g(-1) soil. Soil testing is an important tool for determining the presence of P. brassicae and providing an indication of potential yield loss, e.g., in advisory work on planning for a sustainable OSR crop rotation. This soil test is gaining acceptance as a tool that increases the likelihood of success in precision agriculture and in applied research conducted in commercial oilseed fields and at research stations. The present application highlights the importance of prevention of

In Vitro Activity of Glucosinolates and Their Degradation Products against Brassica-Pathogenic Bacteria and Fungi

PubMed Central

Sotelo, T.; Lema, M.; Soengas, P.; Cartea, M. E.

2014-01-01

Glucosinolates (GSLs) are secondary metabolites found in Brassica vegetables that confer on them resistance against pests and diseases. Both GSLs and glucosinolate hydrolysis products (GHPs) have shown positive effects in reducing soil pathogens. Information about their in vitro biocide effects is scarce, but previous studies have shown sinigrin GSLs and their associated allyl isothiocyanate (AITC) to be soil biocides. The objective of this work was to evaluate the biocide effects of 17 GSLs and GHPs and of leaf methanolic extracts of different GSL-enriched Brassica crops on suppressing in vitro growth of two bacterial (Xanthomonas campestris pv. campestris and Pseudomonas syringae pv. maculicola) and two fungal (Alternaria brassicae and Sclerotinia scletoriorum) Brassica pathogens. GSLs, GHPs, and methanolic leaf extracts inhibited the development of the pathogens tested compared to the control, and the effect was dose dependent. Furthermore, the biocide effects of the different compounds studied were dependent on the species and race of the pathogen. These results indicate that GSLs and their GHPs, as well as extracts of different Brassica species, have potential to inhibit pathogen growth and offer new opportunities to study the use of Brassica crops in biofumigation for the control of multiple diseases. PMID:25362058

Gendered knowledge and adaptive practices: Differentiation and change in Mwanga District, Tanzania.

PubMed

Smucker, Thomas A; Wangui, Elizabeth Edna

2016-12-01

We examine the wider social knowledge domain that complements technical and environmental knowledge in enabling adaptive practices through two case studies in Tanzania. We are concerned with knowledge production that is shaped by gendered exclusion from the main thrusts of planned adaptation, in the practice of irrigation in a dryland village and the adoption of fast-maturing seed varieties in a highland village. The findings draw on data from a household survey, community workshops, and key informant interviews. The largest challenge to effective adaptation is a lack of access to the social networks and institutions that allocate resources needed for adaptation. Results demonstrate the social differentiation of local knowledge, and how it is entwined with adaptive practices that emerge in relation to gendered mechanisms of access. We conclude that community-based adaptation can learn from engaging the broader social knowledge base in evaluating priorities for coping with greater climate variability.

Hedgehog signaling mediates adaptive variation in a dynamic functional system in the cichlid feeding apparatus.

PubMed

Hu, Yinan; Albertson, R Craig

2014-06-10

Adaptive variation in the craniofacial skeleton is a key component of resource specialization and habitat divergence in vertebrates, but the proximate genetic mechanisms that underlie complex patterns of craniofacial variation are largely unknown. Here we demonstrate that the Hedgehog (Hh) signaling pathway mediates widespread variation across a complex functional system that affects the kinematics of lower jaw depression--the opercular four-bar linkage apparatus--among Lake Malawi cichlids. By using a combined quantitative trait locus mapping and population genetics approach, we show that allelic variation in the Hh receptor, ptch1, affects the development of distinct bony elements in the head that represent two of three movable links in this functional system. The evolutionarily derived allele is found in species that feed from the water column, and is associated with shifts in anatomy that translate to a four-bar system capable of faster jaw rotation. Alternatively, the ancestral allele is found in species that feed on attached algae, and is associated with the development of a four-bar system that predicts slower jaw movement. Experimental manipulation of the Hh pathway during cichlid development recapitulates functionally salient natural variation in craniofacial geometry. In all, these results significantly extend our understanding of the mechanisms that fine-tune the craniofacial skeletal complex during adaptation to new foraging niches.

Transcriptomic basis of functional difference and coordination between seeds and the silique wall of Brassica napus during the seed-filling stage.

PubMed

Liu, Han; Yang, Qingyong; Fan, Chuchuan; Zhao, Xiaoqin; Wang, Xuemin; Zhou, Yongming

2015-04-01

The silique of oilseed rape (Brassica napus) is a composite organ including seeds and the silique wall (SW) that possesses distinctly physiological, biochemical and functional differentiations. Yet, the molecular events controlling such differences between the SW and seeds, as well as their coordination during silique development at transcriptional level are largely unknown. Here, we identified large sets of differentially expressed genes in the SW and seeds of siliques at 21-22 days after flowering with a Brassica 95K EST microarray. At this particular stage, there were 3278 SW preferentially expressed genes and 2425 seed preferentially expressed genes. Using the MapMan visualization software, genes differentially regulated in various metabolic pathways and sub-pathways between the SW and seeds were revealed. Photosynthesis and transport-related genes were more actively transcripted in the SW, while those involved in lipid metabolism were more active in seeds during the seed filling stage. On the other hand, genes involved in secondary metabolisms were selectively regulated in the SW and seeds. Large numbers of transcription factors were identified to be differentially expressed between the SW and seeds, suggesting a complex pattern of transcriptional control in these two organs. Furthermore, most genes discussed in categories or pathways showed a similar expression pattern through 21 DAF to 42 DAF. Our results thus provide insights into the coordination of seeds and the SW in the developing silique at the transcriptional levels, which will facilitate the functional studies of important genes for improving B. napus seed productivity and quality. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Plant growth regulator-mediated anti-herbivore responses of cabbage (Brassica oleracea) against cabbage looper Trichoplusia ni Hübner (Lepidoptera: Noctuidae).

PubMed

Scott, Ian M; Samara, R; Renaud, J B; Sumarah, M W

2017-09-01

Plant elicitors can be biological or chemical-derived stimulators of jasmonic acid (JA) or salicylic acid (SA) pathways shown to prime the defenses in many crops. Examples of chemical elicitors of the JA and SA pathways include methyl-jasmonate and 1,2,3-benzothiadiazole-7-carbothioate (BTH or the commercial plant activator Actigard 50WG, respectively). The use of specific elicitors has been observed to affect the normal interaction between JA and SA pathways causing one to be upregulated and the other to be suppressed, often, but not always, at the expense of the plant's herbivore or pathogen defenses. The objective of this study was to determine whether insects feeding on Brassica crops might be negatively affected by SA inducible defenses combined with an inhibitor of detoxification and anti-oxidant enzymes that regulate the insect response to the plant's defenses. The relative growth rate of cabbage looper Trichoplusia ni Hübner (Lepidoptera: Noctuidae) fed induced cabbage Brassica oleraceae leaves with the inhibitor, quercetin, was significantly less than those fed control cabbage with and without the inhibitor. The reduced growth was related to the reduction of glutathione S-transferases (GSTs) by the combination of quercetin and increased levels of indole glucosinolates in the cabbage treated with BTH at 2.6× the recommended application rate. These findings may offer a novel combination of elicitor and synergist that can provide protection from plant disease and herbivores in cabbage and other Brassica crops. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus.

PubMed

Wei, Lijuan; Jian, Hongju; Lu, Kun; Filardo, Fiona; Yin, Nengwen; Liu, Liezhao; Qu, Cunmin; Li, Wei; Du, Hai; Li, Jiana

2016-06-01

Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Genome-wide investigation of genetic changes during modern breeding of Brassica napus.

PubMed

Wang, Nian; Li, Feng; Chen, Biyun; Xu, Kun; Yan, Guixin; Qiao, Jiangwei; Li, Jun; Gao, Guizhen; Bancroft, Ian; Meng, Jingling; King, Graham J; Wu, Xiaoming

2014-08-01

Considerable genome variation had been incorporated within rapeseed breeding programs over past decades. In past decades, there have been substantial changes in phenotypic properties of rapeseed as a result of extensive breeding effort. Uncovering the underlying patterns of allelic variation in the context of genome organisation would provide knowledge to guide future genetic improvement. We assessed genome-wide genetic changes, including population structure, genetic relatedness, the extent of linkage disequilibrium, nucleotide diversity and genetic differentiation based on F ST outlier detection, for a panel of 472 Brassica napus inbred accessions using a 60 k Brassica Infinium® SNP array. We found genetic diversity varied in different sub-groups. Moreover, the genetic diversity increased from 1950 to 1980 and then remained at a similar level in China and Europe. We also found ~6-10 % genomic regions revealed high F ST values. Some QTLs previously associated with important agronomic traits overlapped with these regions. Overall, the B. napus C genome was found to have more high F ST signals than the A genome, and we concluded that the C genome may contribute more valuable alleles to generate elite traits. The results of this study indicate that considerable genome variation had been incorporated within rapeseed breeding programs over past decades. These results also contribute to understanding the impact of rapeseed improvement on available genome variation and the potential for dissecting complex agronomic traits.

Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops

PubMed Central

Saqib, Hafiz Sohaib Ahmed; You, Minsheng

2017-01-01

Conservation biological control emphasizes natural and other non-crop vegetation as a source of natural enemies to focal crops. There is an unmet need for better methods to identify the types of vegetation that are optimal to support specific natural enemies that may colonize the crops. Here we explore the commonality of the spider assemblage—considering abundance and diversity (H)—in brassica crops with that of adjacent non-crop and non-brassica crop vegetation. We employ spatial-based multivariate ordination approaches, hierarchical clustering and spatial eigenvector analysis. The small-scale mixed cropping and high disturbance frequency of southern Chinese vegetation farming offered a setting to test the role of alternate vegetation for spider conservation. Our findings indicate that spider families differ markedly in occurrence with respect to vegetation type. Grassy field margins, non-crop vegetation, taro and sweetpotato harbour spider morphospecies and functional groups that are also present in brassica crops. In contrast, pumpkin and litchi contain spiders not found in brassicas, and so may have little benefit for conservation biological control services for brassicas. Our findings also illustrate the utility of advanced statistical approaches for identifying spatial relationships between natural enemies and the land uses most likely to offer alternative habitats for conservation biological control efforts that generates testable hypotheses for future studies. PMID:29085741

Deciphering the Diploid Ancestral Genome of the Mesohexaploid Brassica rapa[C][W

PubMed Central

Cheng, Feng; Mandáková, Terezie; Wu, Jian; Xie, Qi; Lysak, Martin A.; Wang, Xiaowu

2013-01-01

The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers. PMID:23653472

Induced polyploidization in Brassica campestris L. (Brassicaceae).

PubMed

Kumar, G; Dwivedi, K

2014-01-01

Present experimental design has been made up to obtain crop with higher ploidy level via synthetic polyploidization. Since ploidy manipulation is generally associated with the obtainment of some increased enviable traits of the crop and also provides them greater adaptability to unfavorable or harsh circumstances as compared to its diploids counterparts. Thus, herein present research autotetraploids of Brassica campestris L. have been lucratively achieved by the application of colchicine. Two methods of treatment were utilized i.e. seed treatment and seedling treatment. No polyploidy could be obtained through seed treatment while seedling treatment responded well towards polyploidy. However, the status of autotetraploidy has been confirmed by cytomorphological investigations of treated plants as against its diploids counterparts. For the purpose, morphological parameters such as increased stomata size, pollen diameter, flower size, reproductive organs whereas reduction in plant height, leaf length, leaf breadth, stomata frequency, number of flowers/inflorescence etc. were appraised. Further, cytological observations were made that had clearly revealed the doubling of genome in the autotetraploids as compared to diploids. Meanwhile, pollen fertility and size of pollen grains were evaluated as well.

Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

PubMed Central

Atger, Florian; Gobet, Cédric; Marquis, Julien; Martin, Eva; Wang, Jingkui; Weger, Benjamin; Lefebvre, Grégory; Descombes, Patrick; Naef, Felix; Gachon, Frédéric

2015-01-01

Diurnal oscillations of gene expression are a hallmark of rhythmic physiology across most living organisms. Such oscillations are controlled by the interplay between the circadian clock and feeding rhythms. Although rhythmic mRNA accumulation has been extensively studied, comparatively less is known about their transcription and translation. Here, we quantified simultaneously temporal transcription, accumulation, and translation of mouse liver mRNAs under physiological light–dark conditions and ad libitum or night-restricted feeding in WT and brain and muscle Arnt-like 1 (Bmal1)-deficient animals. We found that rhythmic transcription predominantly drives rhythmic mRNA accumulation and translation for a majority of genes. Comparison of wild-type and Bmal1 KO mice shows that circadian clock and feeding rhythms have broad impact on rhythmic gene expression, Bmal1 deletion affecting surprisingly both transcriptional and posttranscriptional levels. Translation efficiency is differentially regulated during the diurnal cycle for genes with 5′-Terminal Oligo Pyrimidine tract (5′-TOP) sequences and for genes involved in mitochondrial activity, many harboring a Translation Initiator of Short 5′-UTR (TISU) motif. The increased translation efficiency of 5′-TOP and TISU genes is mainly driven by feeding rhythms but Bmal1 deletion also affects amplitude and phase of translation, including TISU genes. Together this study emphasizes the complex interconnections between circadian and feeding rhythms at several steps ultimately determining rhythmic gene expression and translation. PMID:26554015

Adaptive Control of a Transport Aircraft Using Differential Thrust

NASA Technical Reports Server (NTRS)

Stepanyan, Vahram; Krishnakumar, Kalmanje; Nguyen, Nhan

2009-01-01

The paper presents an adaptive control technique for a damaged large transport aircraft subject to unknown atmospheric disturbances such as wind gust or turbulence. It is assumed that the damage results in vertical tail loss with no rudder authority, which is replaced with a differential thrust input. The proposed technique uses the adaptive prediction based control design in conjunction with the time scale separation principle, based on the singular perturbation theory. The application of later is necessitated by the fact that the engine response to a throttle command is substantially slow that the angular rate dynamics of the aircraft. It is shown that this control technique guarantees the stability of the closed-loop system and the tracking of a given reference model. The simulation example shows the benefits of the approach.

Multi Sensor Fusion Using Fitness Adaptive Differential Evolution

NASA Astrophysics Data System (ADS)

Giri, Ritwik; Ghosh, Arnob; Chowdhury, Aritra; Das, Swagatam

The rising popularity of multi-source, multi-sensor networks supports real-life applications calls for an efficient and intelligent approach to information fusion. Traditional optimization techniques often fail to meet the demands. The evolutionary approach provides a valuable alternative due to its inherent parallel nature and its ability to deal with difficult problems. We present a new evolutionary approach based on a modified version of Differential Evolution (DE), called Fitness Adaptive Differential Evolution (FiADE). FiADE treats sensors in the network as distributed intelligent agents with various degrees of autonomy. Existing approaches based on intelligent agents cannot completely answer the question of how their agents could coordinate their decisions in a complex environment. The proposed approach is formulated to produce good result for the problems that are high-dimensional, highly nonlinear, and random. The proposed approach gives better result in case of optimal allocation of sensors. The performance of the proposed approach is compared with an evolutionary algorithm coordination generalized particle model (C-GPM).

In vitro activity of glucosinolates and their degradation products against brassica-pathogenic bacteria and fungi.

PubMed

Sotelo, T; Lema, M; Soengas, P; Cartea, M E; Velasco, P

2015-01-01

Glucosinolates (GSLs) are secondary metabolites found in Brassica vegetables that confer on them resistance against pests and diseases. Both GSLs and glucosinolate hydrolysis products (GHPs) have shown positive effects in reducing soil pathogens. Information about their in vitro biocide effects is scarce, but previous studies have shown sinigrin GSLs and their associated allyl isothiocyanate (AITC) to be soil biocides. The objective of this work was to evaluate the biocide effects of 17 GSLs and GHPs and of leaf methanolic extracts of different GSL-enriched Brassica crops on suppressing in vitro growth of two bacterial (Xanthomonas campestris pv. campestris and Pseudomonas syringae pv. maculicola) and two fungal (Alternaria brassicae and Sclerotinia scletoriorum) Brassica pathogens. GSLs, GHPs, and methanolic leaf extracts inhibited the development of the pathogens tested compared to the control, and the effect was dose dependent. Furthermore, the biocide effects of the different compounds studied were dependent on the species and race of the pathogen. These results indicate that GSLs and their GHPs, as well as extracts of different Brassica species, have potential to inhibit pathogen growth and offer new opportunities to study the use of Brassica crops in biofumigation for the control of multiple diseases. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Egg Laying of Cabbage White Butterfly (Pieris brassicae) on Arabidopsis thaliana Affects Subsequent Performance of the Larvae

PubMed Central

Blenn, Beatrice; Drechsler, Navina; Gershenzon, Jonathan; Kunze, Reinhard; Hilker, Monika

2013-01-01

Plant resistance to the feeding by herbivorous insects has recently been found to be positively or negatively influenced by prior egg deposition. Here we show how crucial it is to conduct experiments on plant responses to herbivory under conditions that simulate natural insect behaviour. We used a well-studied plant – herbivore system, Arabidopsis thaliana and the cabbage white butterfly Pieris brassicae, testing the effects of naturally laid eggs (rather than egg extracts) and allowing larvae to feed gregariously as they do naturally (rather than placing single larvae on plants). Under natural conditions, newly hatched larvae start feeding on their egg shells before they consume leaf tissue, but access to egg shells had no effect on subsequent larval performance in our experiments. However, young larvae feeding gregariously on leaves previously laden with eggs caused less feeding damage, gained less weight during the first 2 days, and suffered twice as high a mortality until pupation compared to larvae feeding on plants that had never had eggs. The concentration of the major anti-herbivore defences of A. thaliana, the glucosinolates, was not significantly increased by oviposition, but the amount of the most abundant member of this class, 4-methylsulfinylbutyl glucosinolate was 1.8-fold lower in larval-damaged leaves with prior egg deposition compared to damaged leaves that had never had eggs. There were also few significant changes in the transcript levels of glucosinolate metabolic genes, except that egg deposition suppressed the feeding-induced up-regulation of FMOGS-OX2, a gene encoding a flavin monooxygenase involved in the last step of 4-methylsulfinylbutyl glucosinolate biosynthesis. Hence, our study demonstrates that oviposition does increase A. thaliana resistance to feeding by subsequently hatching larvae, but this cannot be attributed simply to changes in glucosinolate content. PMID:23527243

Improvement of tissue culture, genetic transformation, and applications of biotechnology to Brassica.

PubMed

Ravanfar, Seyed Ali; Orbovic, Vladimir; Moradpour, Mahdi; Abdul Aziz, Maheran; Karan, Ratna; Wallace, Simon; Parajuli, Saroj

2017-04-01

Development of in vitro plant regeneration method from Brassica explants via organogenesis and somatic embryogenesis is influenced by many factors such as culture environment, culture medium composition, explant sources, and genotypes which are reviewed in this study. An efficient in vitro regeneration system to allow genetic transformation of Brassica is a crucial tool for improving its economical value. Methods to optimize transformation protocols for the efficient introduction of desirable traits, and a comparative analysis of these methods are also reviewed. Hence, binary vectors, selectable marker genes, minimum inhibitory concentration of selection agents, reporter marker genes, preculture media, Agrobacterium concentration and regeneration ability of putative transformants for improvement of Agrobacterium-mediated transformation of Brassica are discussed.

Transfer of sclerotinia resistance from wild relative of Brassica oleracea into Brassica napus using a hexaploidy step.

PubMed

Mei, Jiaqin; Liu, Yao; Wei, Dayong; Wittkop, Benjamin; Ding, Yijuan; Li, Qinfei; Li, Jiana; Wan, Huafang; Li, Zaiyun; Ge, Xianhong; Frauen, Martin; Snowdon, Rod J; Qian, Wei; Friedt, Wolfgang

2015-04-01

Sclerotinia resistance was transferred into rapeseed from a wild relative of Brassica oleracea (B. incana) using hexaploids derived from crosses between B. incana and rapeseed as a bridge. A high level of resistance against Sclerotinia sclerotiorum has been documented in wild Brassica oleracea, but not in cultivated rapeseed (Brassica napus). To transfer sclerotinia resistance from a wild relative into rapeseed, a strategy was proposed using hexaploids (AACCCC) derived from crosses between the wild B. oleracea-related B. incana genotype 'C01' and the Chinese rapeseed variety 'Zhongshuang 9' as a bridge. Progenies (BC1F1) generated by backcrossing the hexaploid to 'Zhongshuang 9' could be generated with a high crossability (average 18.3 seeds per pod). Seventy-three individuals in BC1F1 were firstly screened for resistance with five molecular markers linked to the major resistance QTL on chromosome C09 in 'C01', and 11 individuals harboring resistance loci were selected to develop vegetative clones. Of these, five exhibited significantly higher resistance than 'Zhongshuang 9' and the most resistant individual was chosen to develop the BC1F2 progeny. Finally, five individual genotypes with nearly twofold higher resistance than 'Zhongshuang 9' were found among 100 BC1F2 individuals by using marker-assisted selection and resistance evaluation. Hereof, one rapeseed-type individual with 38 chromosomes and good self-fertility (15.0 ± 3.56 seeds/pod) was identified. Our results indicate that the proposed strategy is effective for transferring sclerotinia resistance from a wild relative of B. oleracea into rapeseed.

Differential expression of feeding-related hypothalamic neuropeptides in the first generation of quails divergently selected for low or high feed efficiency.

PubMed

Blankenship, Kaley; Gilley, Alex; Piekarski, Alissa; Orlowski, Sara; Greene, Elizabeth; Bottje, Walter; Anthony, Nicholas; Dridi, Sami

2016-08-01

Livestock and poultry sectors are facing a combination of challenges, including a substantial increase in global demand for high quality animal protein, general droughts and steady rise in animal feed cost. Thus feed efficiency (FE), which defines the animal's ability to convert feed into body weight, is a vital economic and agricultural trait. Genetic selection for FE has been largely used in chickens and has been applied without knowledge of the underlying molecular mechanisms. Although it has made tremendous progress (breast yield, growth rate, egg production), there have been a number of undesirable changes such as metabolic disorders. In the present study we divergently selected male and female quail for high and low FE and we aimed to characterize the molecular basis of these differences at the central level, with the long-term goal of maximizing FE and avoiding the unfavorable consequences. The FE phenotype in first generation quails seemed to be achieved by reduced feed intake in female and increased body weight gain in males. At the molecular level, we found that the expression of feeding-related hypothalamic genes is gender- and line-dependent. Indeed, the expression of NPY, POMC, CART, CRH, melanocortin system (MC1R, MC2R, MC4R, MC5R), ORX, mTOR and ACCα was significantly decreased, however ORXR1/2, AMPKα1, S6K1 and STAT1, 5 and 6 were increased in high compared to low FE males (P<0.05). These genes did not differ between the two female lines. ADPN gene expression was higher and its receptor Adip-R1 was lower in LFE compared to HFE females (P<0.05). In male however, although there was no difference in ADPN gene expression between the genotypes, Adip-R1 and Adip-R2 mRNA abundances were higher in the LFE compared to HFE line (P<0.05). This study identified several key central feeding-related genes that are differentially expressed between low and high FE male and female quails which might explain the differences in feed intake/body weight gain observed

Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica

PubMed Central

2011-01-01

Background Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these cannot easily explain, however, how the diverse mitotypes evolved within each genus or species. We analyzed the evolutionary relationships of Brassica mitotypes by sequencing. Results We sequenced the mitotypes of cam (Brassica rapa), ole (B. oleracea), jun (B. juncea), and car (B. carinata) and analyzed them together with two previously sequenced mitotypes of B. napus (pol and nap). The sizes of whole single circular genomes of cam, jun, ole, and car are 219,747 bp, 219,766 bp, 360,271 bp, and 232,241 bp, respectively. The mitochondrial genome of ole is largest as a resulting of the duplication of a 141.8 kb segment. The jun mitotype is the result of an inherited cam mitotype, and pol is also derived from the cam mitotype with evolutionary modifications. Genes with known functions are conserved in all mitotypes, but clear variation in open reading frames (ORFs) with unknown functions among the six mitotypes was observed. Sequence relationship analysis showed that there has been genome compaction and inheritance in the course of Brassica mitotype evolution. Conclusions We have sequenced four Brassica mitotypes, compared six Brassica mitotypes and suggested a mechanism for mitochondrial genome formation in Brassica, including evolutionary events such as inheritance, duplication, rearrangement, genome compaction, and mutation. PMID:21988783

Bolbase: a comprehensive genomics database for Brassica oleracea.

PubMed

Yu, Jingyin; Zhao, Meixia; Wang, Xiaowu; Tong, Chaobo; Huang, Shunmou; Tehrim, Sadia; Liu, Yumei; Hua, Wei; Liu, Shengyi

2013-09-30

Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, kohlrabi, kale, Brussels sprouts. This diversity along with its phylogenetic membership in a group of three diploid and three tetraploid species, and the recent availability of genome sequences within Brassica provide an unprecedented opportunity to study intra- and inter-species divergence and evolution in this species and its close relatives. We have developed a comprehensive database, Bolbase, which provides access to the B. oleracea genome data and comparative genomics information. The whole genome of B. oleracea is available, including nine fully assembled chromosomes and 1,848 scaffolds, with 45,758 predicted genes, 13,382 transposable elements, and 3,581 non-coding RNAs. Comparative genomics information is available, including syntenic regions among B. oleracea, Brassica rapa and Arabidopsis thaliana, synonymous (Ks) and non-synonymous (Ka) substitution rates between orthologous gene pairs, gene families or clusters, and differences in quantity, category, and distribution of transposable elements on chromosomes. Bolbase provides useful search and data mining tools, including a keyword search, a local BLAST server, and a customized GBrowse tool, which can be used to extract annotations of genome components, identify similar sequences and visualize syntenic regions among species. Users can download all genomic data and explore comparative genomics in a highly visual setting. Bolbase is the first resource platform for the B. oleracea genome and for genomic comparisons with its relatives, and thus it will help the research community to better study the function and evolution of Brassica genomes as well as enhance molecular breeding research. This database will be updated regularly with new features, improvements to genome annotation, and new genomic sequences as they

Bolbase: a comprehensive genomics database for Brassica oleracea

PubMed Central

2013-01-01

Background Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, kohlrabi, kale, Brussels sprouts. This diversity along with its phylogenetic membership in a group of three diploid and three tetraploid species, and the recent availability of genome sequences within Brassica provide an unprecedented opportunity to study intra- and inter-species divergence and evolution in this species and its close relatives. Description We have developed a comprehensive database, Bolbase, which provides access to the B. oleracea genome data and comparative genomics information. The whole genome of B. oleracea is available, including nine fully assembled chromosomes and 1,848 scaffolds, with 45,758 predicted genes, 13,382 transposable elements, and 3,581 non-coding RNAs. Comparative genomics information is available, including syntenic regions among B. oleracea, Brassica rapa and Arabidopsis thaliana, synonymous (Ks) and non-synonymous (Ka) substitution rates between orthologous gene pairs, gene families or clusters, and differences in quantity, category, and distribution of transposable elements on chromosomes. Bolbase provides useful search and data mining tools, including a keyword search, a local BLAST server, and a customized GBrowse tool, which can be used to extract annotations of genome components, identify similar sequences and visualize syntenic regions among species. Users can download all genomic data and explore comparative genomics in a highly visual setting. Conclusions Bolbase is the first resource platform for the B. oleracea genome and for genomic comparisons with its relatives, and thus it will help the research community to better study the function and evolution of Brassica genomes as well as enhance molecular breeding research. This database will be updated regularly with new features, improvements to genome annotation

Light influence in the nutritional composition of Brassica oleracea sprouts.

PubMed

Vale, A P; Santos, J; Brito, N V; Peixoto, V; Carvalho, Rosa; Rosa, E; Oliveira, M Beatriz P P

2015-07-01

Brassica sprouts are considered a healthy food product, whose nutritional quality can be influenced by several factors. The aim of this work was to monitor the nutritional composition changes promoted by different sprouting conditions of four varieties of Brassica oleracea (red cabbage, broccoli, Galega kale and Penca cabbage). Sprouts were grown under light/darkness cycles and complete darkness. Standard AOAC methods were applied for nutritional value evaluation, while chromatographic methods with UV-VIS and FID detection were used to determine the free amino acids and fatty acids, respectively. Mineral content was analyzed by atomic absorption spectrometry. Sprouts composition revealed them as an excellent source of protein and dietary fiber. Selenium content was one of the most distinctive feature of sprouts, being the sprouting conditions determinant for the free amino acid and fatty acids profile. The use of complete darkness was beneficial to the overall nutritional quality of the brassica sprouts studied. Copyright © 2015 Elsevier Ltd. All rights reserved.

Oestradiol differentially influences feeding behaviour depending on diet composition in female rhesus monkeys

PubMed Central

Johnson, ZP; Lowe, J; Michopoulos, V; Moore, CJ; Wilson, ME; Toufexis, D

2015-01-01

In females, cyclical changes in the ovarian hormone oestradiol are known to modulate feeding behaviour. However, what is less clear is how these behavioural effects of oestradiol are modified by the macronutrient content of a diet. Here we present data showing that oestradiol treatment results in both significantly smaller meals and reduced total caloric intake in ovariectomised, socially housed female rhesus macaques when only chow diet is available. Conversely, during a choice dietary condition where both palatable and chow options are available, oestradiol treatment had no observable, attenuating effect on caloric intake. During this choice dietary phase, all animals consumed more of the palatable diet than chow diet; however, oestradiol treatment appeared to further increase preference for the palatable diet. Finally, oestradiol treatment increased snacking behaviour, i.e. consumption of calories outside of empirically defined meals, regardless of diet condition. These findings illustrate how oestradiol differentially influences feeding behaviour depending on the dietary environment and provides a framework in which we can begin to examine the mechanisms underlying these observed changes. PMID:23714578

Profiling Polyphenols in Five Brassica species Microgreens by UHPLC-PDA-ESI/HRMSn

PubMed Central

Sun, Jianghao; Xiao, Zhenlei; Lin, Long-ze; Lester, Gene E.; Wang, Qin; Harnly, James M.; Chen, Pei

2014-01-01

Brassica vegetables are known to contain relatively high concentrations of bioactive compounds associated with human health. A comprehensive profiling of polyphenols from five Brassica species microgreens was conducted using ultra high-performance liquid chromatography photo diode array high-resolution multi-stage mass spectrometry (UHPLC-PDA-ESI/HRMSn). A total of 164 polyphenols including 30 anthocyanins, 105 flavonol glycosides, and 29 hydroxycinnamic acid and hydroxybenzoic acid derivatives were putatively identified.The putative identifications were based on UHPLC-HRMSn analysis using retention times, elution orders, UV/Vis spectra and high resolution mass spectra, in-house polyphenol database, and as well as literature comparisons. This study showed that these five Brassica species microgreens could be considered as good sources of food polyphenols. PMID:24144328

Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus

PubMed Central

Obermeier, Christian; Hosseini, Bashir; Friedt, Wolfgang; Snowdon, Rod

2009-01-01

Background Serial analysis of gene expression (LongSAGE) was applied for gene expression profiling in seeds of oilseed rape (Brassica napus ssp. napus). The usefulness of this technique for detailed expression profiling in a non-model organism was demonstrated for the highly complex, neither fully sequenced nor annotated genome of B. napus by applying a tag-to-gene matching strategy based on Brassica ESTs and the annotated proteome of the closely related model crucifer A. thaliana. Results Transcripts from 3,094 genes were detected at two time-points of seed development, 23 days and 35 days after pollination (DAP). Differential expression showed a shift from gene expression involved in diverse developmental processes including cell proliferation and seed coat formation at 23 DAP to more focussed metabolic processes including storage protein accumulation and lipid deposition at 35 DAP. The most abundant transcripts at 23 DAP were coding for diverse protease inhibitor proteins and proteases, including cysteine proteases involved in seed coat formation and a number of lipid transfer proteins involved in embryo pattern formation. At 35 DAP, transcripts encoding napin, cruciferin and oleosin storage proteins were most abundant. Over both time-points, 18.6% of the detected genes were matched by Brassica ESTs identified by LongSAGE tags in antisense orientation. This suggests a strong involvement of antisense transcript expression in regulatory processes during B. napus seed development. Conclusion This study underlines the potential of transcript tagging approaches for gene expression profiling in Brassica crop species via EST matching to annotated A. thaliana genes. Limits of tag detection for low-abundance transcripts can today be overcome by ultra-high throughput sequencing approaches, so that tag-based gene expression profiling may soon become the method of choice for global expression profiling in non-model species. PMID:19575793

Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

PubMed

Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

2015-01-01

The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/. © The Author(s) 2015. Published by Oxford University Press.

Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce

PubMed Central

Namroud, Marie-Claire; Beaulieu, Jean; Juge, Nicolas; Laroche, Jérôme; Bousquet, Jean

2008-01-01

Conifers are characterized by a large genome size and a rapid decay of linkage disequilibrium, most often within gene limits. Genome scans based on noncoding markers are less likely to detect molecular adaptation linked to genes in these species. In this study, we assessed the effectiveness of a genome-wide single nucleotide polymorphism (SNP) scan focused on expressed genes in detecting local adaptation in a conifer species. Samples were collected from six natural populations of white spruce (Picea glauca) moderately differentiated for several quantitative characters. A total of 534 SNPs representing 345 expressed genes were analysed. Genes potentially under natural selection were identified by estimating the differentiation in SNP frequencies among populations (FST) and identifying outliers, and by estimating local differentiation using a Bayesian approach. Both average expected heterozygosity and population differentiation estimates (HE = 0.270 and FST = 0.006) were comparable to those obtained with other genetic markers. Of all genes, 5.5% were identified as outliers with FST at the 95% confidence level, while 14% were identified as candidates for local adaptation with the Bayesian method. There was some overlap between the two gene sets. More than half of the candidate genes for local adaptation were specific to the warmest population, about 20% to the most arid population, and 15% to the coldest and most humid higher altitude population. These adaptive trends were consistent with the genes’ putative functions and the divergence in quantitative traits noted among the populations. The results suggest that an approach separating the locus and population effects is useful to identify genes potentially under selection. These candidates are worth exploring in more details at the physiological and ecological levels. PMID:18662225

On the adaptivity and complexity embedded into differential evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Senkerik, Roman; Pluhacek, Michal; Jasek, Roman

2016-06-08

This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performedmore » on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.« less

Enteric methane production and ruminal fermentation from forage brassica diets fed in continuous culture

USDA-ARS?s Scientific Manuscript database

Brassicas provide forage for livestock during the late fall when traditional perennial cool-season forages are not productive. However, little research exists on ruminal fermentation and methane(CH4) production of brassicas fed as forage. A continuous culture fermentor system was used to assess nutr...

An Efficient Method for Adventitious Root Induction from Stem Segments of Brassica Species

PubMed Central

Srikanth, Sandhya; Choong, Tsui Wei; Yan, An; He, Jie; Chen, Zhong

2016-01-01

Plant propagation via in vitro culture is a very laborious and time-consuming process. The growth cycle of some of the crop species is slow even in the field and the consistent commercial production is hard to maintain. Enhanced methods of reduced cost, materials and labor significantly impact the research and commercial production of field crops. In our studies, stem-segment explants of Brassica species were found to generate adventitious roots (AR) in aeroponic systems in less than a week. As such, the efficiency of rooting from stem explants of six cultivar varieties of Brassica spp was tested without using any plant hormones. New roots and shoots were developed from Brassica alboglabra (Kai Lan), B. oleracea var. acephala (purple kale), B. rapa L. ssp. chinensis L (Pai Tsai, Nai Bai C, and Nai Bai T) explants after 3 to 5 days of growing under 20 ± 2°C cool root zone temperature (C-RZT) and 4 to 7 days in 30 ± 2°C ambient root zone temperature (A-RZT). At the base of cut end, anticlinal and periclinal divisions of the cambial cells resulted in secondary xylem toward pith and secondary phloem toward cortex. The continuing mitotic activity of phloem parenchyma cells led to a ring of conspicuous white callus. Root initials formed from the callus which in turn developed into ARs. However, B. rapa var. nipposinica (Mizuna) explants were only able to root in C-RZT. All rooted explants were able to develop into whole plants, with higher biomass obtained from plants that grown in C-RZT. Moreover, explants from both RZTs produced higher biomass than plants grown from seeds (control plants). Rooting efficiency was affected by RZTs and explant cuttings of donor plants. Photosynthetic CO2 assimilation rate (Asat) and stomatal conductance (gssat) were significantly differentiated between plants derived from seeds and explants at both RZTs. All plants in A-RZT had highest transpiration rates. PMID:27446170

Antimicrobial effect against different bacterial strains and bacterial adaptation to essential oils used as feed additives.

PubMed

Melo, Antonio Diego Brandão; Amaral, Amanda Figueiredo; Schaefer, Gustavo; Luciano, Fernando Bittencourt; de Andrade, Carla; Costa, Leandro Batista; Rostagno, Marcos Horácio

2015-10-01

The aim of this study was to evaluate the antimicrobial activity and determine the minimum bactericidal concentration (MBC) of the essential oils derived from Origanum vulgare (oregano), Melaleuca alternifolia (tea tree), Cinnamomum cassia (cassia), and Thymus vulgaris (white thyme) against Salmonella Typhimurium, Salmonella Enteritidis, Escherichia coli, Staphylococcus aureus and Enterococcus faecalis. The study also investigated the ability of these different bacterial strains to develop adaptation after repetitive exposure to sub-lethal concentrations of these essential oils. The MBC of the essential oils studied was determined by disc diffusion and broth dilution methods. All essential oils showed antimicrobial effect against all bacterial strains. In general, the development of adaptation varied according to the bacterial strain and the essential oil (tea tree > white thyme > oregano). Therefore, it is important to use essential oils at efficient bactericidal doses in animal feed, food, and sanitizers, since bacteria can rapidly develop adaptation when exposed to sub-lethal concentrations of these oils.

Antimicrobial effect against different bacterial strains and bacterial adaptation to essential oils used as feed additives

PubMed Central

Melo, Antonio Diego Brandão; Amaral, Amanda Figueiredo; Schaefer, Gustavo; Luciano, Fernando Bittencourt; de Andrade, Carla; Costa, Leandro Batista; Rostagno, Marcos Horácio

2015-01-01

The aim of this study was to evaluate the antimicrobial activity and determine the minimum bactericidal concentration (MBC) of the essential oils derived from Origanum vulgare (oregano), Melaleuca alternifolia (tea tree), Cinnamomum cassia (cassia), and Thymus vulgaris (white thyme) against Salmonella Typhimurium, Salmonella Enteritidis, Escherichia coli, Staphylococcus aureus and Enterococcus faecalis. The study also investigated the ability of these different bacterial strains to develop adaptation after repetitive exposure to sub-lethal concentrations of these essential oils. The MBC of the essential oils studied was determined by disc diffusion and broth dilution methods. All essential oils showed antimicrobial effect against all bacterial strains. In general, the development of adaptation varied according to the bacterial strain and the essential oil (tea tree > white thyme > oregano). Therefore, it is important to use essential oils at efficient bactericidal doses in animal feed, food, and sanitizers, since bacteria can rapidly develop adaptation when exposed to sub-lethal concentrations of these oils. PMID:26424908

Productivity and nutritive quality of three brassica varieties for use in pasture-based systems

USDA-ARS?s Scientific Manuscript database

Brassicas are gaining popularity among pasture-based livestock producers to extend grazing during the ‘summer slump’ and throughout the fall. A 2-yr study was conducted to compare biomass production and nutrient composition of ‘Barisca’ rapeseed (RAP; Brassica napus L.), ‘Inspiration’ canola (CAN; B...

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis.

PubMed

Herrera, Carlos M; Bazaga, Pilar

2010-08-01

*In plants, epigenetic variations based on DNA methylation are often heritable and could influence the course of evolution. Before this hypothesis can be assessed, fundamental questions about epigenetic variation remain to be addressed in a real-world context, including its magnitude, structuring within and among natural populations, and autonomy in relation to the genetic context. *Extent and patterns of cytosine methylation, and the relationship to adaptive genetic divergence between populations, were investigated for wild populations of the southern Spanish violet Viola cazorlensis (Violaceae) using the methylation-sensitive amplified polymorphism (MSAP) technique, a modification of the amplified fragment length polymorphism method (AFLP) based on the differential sensitivity of isoschizomeric restriction enzymes to site-specific cytosine methylation. *The genome of V. cazorlensis plants exhibited extensive levels of methylation, and methylation-based epigenetic variation was structured into distinct between- and within- population components. Epigenetic differentiation of populations was correlated with adaptive genetic divergence revealed by a Bayesian population-genomic analysis of AFLP data. Significant associations existed at the individual genome level between adaptive AFLP loci and the methylation state of methylation-susceptible MSAP loci. *Population-specific, divergent patterns of correlated selection on epigenetic and genetic individual variation could account for the coordinated epigenetic-genetic adaptive population differentiation revealed by this study.

QTL analysis of root morphology, flowering time, and yield reveals trade-offs in response to drought in Brassica napus.

PubMed

Fletcher, Richard S; Mullen, Jack L; Heiliger, Annie; McKay, John K

2015-01-01

Drought escape and dehydration avoidance represent alternative strategies for drought adaptation in annual crops. The mechanisms underlying these two strategies are reported to have a negative correlation, suggesting a trade-off. We conducted a quantitative trait locus (QTL) analysis of flowering time and root mass, traits representing each strategy, in Brassica napus to understand if a trade-off exists and what the genetic basis might be. Our field experiment used a genotyped population of doubled haploid lines and included both irrigated and rainfed treatments, allowing analysis of plasticity in each trait. We found strong genetic correlations among all traits, suggesting a trade-off among traits may exist. Summing across traits and treatments we found 20 QTLs, but many of these co-localized to two major QTLs, providing evidence that the trade-off is genetically constrained. To understand the mechanistic relationship between root mass, flowering time, and QTLs, we analysed the data by conditioning upon correlated traits. Our results suggest a causal model where such QTLs affect root mass directly as well as through their impacts on flowering time. Additionally, we used draft Brassica genomes to identify orthologues of well characterized Arabidopsis thaliana flowering time genes as candidate genes. This research provides valuable clues to breeding for drought adaptation as it is the first to analyse the inheritance of the root system in B. napus in relation to drought. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Anthocyanidins and polyphenols in five brassica species microgreens: analysis by UHPLC-PDA-ESI/HRMS/MSn

USDA-ARS?s Scientific Manuscript database

Brassica vegetables are known to contain relatively high concentrations of bioactive compounds associated with human health. A comprehensive profiling of polyphenols from five Brassica species microgreens was conducted using ultra high-performance liquid chromatography photo diode array high-resolu...

Health Promoting Effects of Brassica-Derived Phytochemicals: From Chemopreventive and Anti-Inflammatory Activities to Epigenetic Regulation

PubMed Central

Wagner, Anika Eva; Terschluesen, Anna Maria; Rimbach, Gerald

2013-01-01

A high intake of brassica vegetables may be associated with a decreased chronic disease risk. Health promoting effects of Brassicaceae have been partly attributed to glucosinolates and in particular to their hydrolyzation products including isothiocyanates. In vitro and in vivo studies suggest a chemopreventive activity of isothiocyanates through the redox-sensitive transcription factor Nrf2. Furthermore, studies in cultured cells, in laboratory rodents, and also in humans support an anti-inflammatory effect of brassica-derived phytochemicals. However, the underlying mechanisms of how these compounds mediate their health promoting effects are yet not fully understood. Recent findings suggest that brassica-derived compounds are regulators of epigenetic mechanisms. It has been shown that isothiocyanates may inhibit histone deacetylase transferases and DNA-methyltransferases in cultured cells. Only a few papers have dealt with the effect of brassica-derived compounds on epigenetic mechanisms in laboratory animals, whereas data in humans are currently lacking. The present review aims to summarize the current knowledge regarding the biological activities of brassica-derived phytochemicals regarding chemopreventive, anti-inflammatory, and epigenetic pathways. PMID:24454992

Genomic analysis of differentiation between soil types reveals candidate genes for local adaptation in Arabidopsis lyrata.

PubMed

Turner, Thomas L; von Wettberg, Eric J; Nuzhdin, Sergey V

2008-09-11

Serpentine soil, which is naturally high in heavy metal content and has low calcium to magnesium ratios, comprises a difficult environment for most plants. An impressive number of species are endemic to serpentine, and a wide range of non-endemic plant taxa have been shown to be locally adapted to these soils. Locating genomic polymorphisms which are differentiated between serpentine and non-serpentine populations would provide candidate loci for serpentine adaptation. We have used the Arabidopsis thaliana tiling array, which has 2.85 million probes throughout the genome, to measure genetic differentiation between populations of Arabidopsis lyrata growing on granitic soils and those growing on serpentinic soils. The significant overrepresentation of genes involved in ion transport and other functions provides a starting point for investigating the molecular basis of adaptation to soil ion content, water retention, and other ecologically and economically important variables. One gene in particular, calcium-exchanger 7, appears to be an excellent candidate gene for adaptation to low CaratioMg ratio in A. lyrata.

Differentially Fed Metal Frame Antenna With Common Mode Suppression for Biomedical Smartband Applications

NASA Astrophysics Data System (ADS)

Xu, Li-Jie; Duan, Zhu

2018-04-01

This paper proposes a differentially fed metal frame antenna for biomedical smartband applications. It occupies a planar area of 40 × 20 mm, operating at 2.45-GHz industrial, scientific, and medical band. The proposed antenna is composed of an external metal frame and an internal metal box acting as ground for electronics. Through a differential feeding to two copper strips located between the metal frame and the metal box, a rectangular ring slot is excited with common mode suppression capability. The antenna prototype is designed in free space, and then adapted to on-body scenario for both repeater and transmitter cases. Additionally, the proposed differential feeding is modified to the traditional single port, demonstrating the half-size miniaturization technique. Finally, the simulated results are verified by measurement. The proposed antenna's simple structure and satisfactory performance makes it a perfect candidate for future medical smartband applications, monitoring the physiological parameters of humans for health-care purposes.

Brassica cover crops for nitrogen retention in the Mid-Atlantic coastal plain.

PubMed

Dean, Jill E; Weil, Ray R

2009-01-01

Brassica cover crops are new to the mid-Atlantic region, and limited information is available on their N uptake capabilities for effective N conservation. Forage radish (Raphanus sativus L. cv. Daikon), oilseed radish (Raphanus sativus L. cv. Adagio), and rape (Brassica napus L. cv. Dwarf Essex) were compared with rye (Secale cereale L. cv. Wheeler), a popular cover crop in the region, with regard to N uptake ability and potential to decrease N leaching at two sites in Maryland. Plants were harvested in fall and spring for dry matter and N analysis. Soil samples from 0 cm to 105 to 180 cm depth were obtained in fall and spring for NH(4)-N and NO(3)-N analyses. Ceramic cup tension lysimeters were installed at depths of 75 to 120 cm to monitor NO(3)-N in soil pore water. Averaged across 3 site-years, forage radish and rape shoots had greater dry matter production and captured more N in fall than rye shoots. Compared with a weedy fallow control, rape and rye caused similar decreases in soil NO(3)-N in fall and spring throughout the sampled profile. Cover crops had no effect on soil NH(4)-N. During the spring on coarse textured soil, pore water NO(3)-N concentrations in freeze-killed Brassica (radish) plots were greater than in control and overwintering Brassica (rape) and rye plots. On fine textured soil, all cover crops provided a similar decrease in pore water NO(3)-N concentration compared with control. On coarse textured soils, freeze-killed Brassica cover crops should be followed by an early-planted spring main crop.

Consequences of gene flow between oilseed rape (Brassica napus) and its relatives.

PubMed

Liu, Yongbo; Wei, Wei; Ma, Keping; Li, Junsheng; Liang, Yuyong; Darmency, Henri

2013-10-01

Numerous studies have focused on the probability of occurrence of gene flow between transgenic crops and their wild relatives and the likelihood of transgene escape, which should be assessed before the commercial release of transgenic crops. This review paper focuses on this issue for oilseed rape, Brassica napus L., a species that produces huge numbers of pollen grains and seeds. We analyze separately the distinct steps of gene flow: (1) pollen and seeds as vectors of gene flow; (2) spontaneous hybridization; (3) hybrid behavior, fitness cost due to hybridization and mechanisms of introgression; (4) and fitness benefit due to transgenes (e.g. herbicide resistance and Bt toxin). Some physical, biological and molecular means of transgene containment are also described. Although hybrids and first generation progeny are difficult to identify in fields and non-crop habitats, the literature shows that transgenes could readily introgress into Brassica rapa, Brassica juncea and Brassica oleracea, while introgression is expected to be rare with Brassica nigra, Hirschfeldia incana and Raphanus raphanistrum. The hybrids grow well but produce less seed than their wild parent. The difference declines with increasing generations. However, there is large uncertainty about the evolution of chromosome numbers and recombination, and many parameters of life history traits of hybrids and progeny are not determined with satisfactory confidence to build generic models capable to really cover the wide diversity of situations. We show that more studies are needed to strengthen and organize biological knowledge, which is a necessary prerequisite for model simulations to assess the practical and evolutionary outputs of introgression, and to provide guidelines for gene flow management. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Aquaporin water channel AgAQP1 in the malaria vector mosquito Anopheles gambiae during blood feeding and humidity adaptation

PubMed Central

Liu, Kun; Tsujimoto, Hitoshi; Cha, Sung-Jae; Agre, Peter; Rasgon, Jason L.

2011-01-01

Altered patterns of malaria endemicity reflect, in part, changes in feeding behavior and climate adaptation of mosquito vectors. Aquaporin (AQP) water channels are found throughout nature and confer high-capacity water flow through cell membranes. The genome of the major malaria vector mosquito Anopheles gambiae contains at least seven putative AQP sequences. Anticipating that transmembrane water movements are important during the life cycle of A. gambiae, we identified and characterized the A. gambiae aquaporin 1 (AgAQP1) protein that is homologous to AQPs known in humans, Drosophila, and sap-sucking insects. When expressed in Xenopus laevis oocytes, AgAQP1 transports water but not glycerol. Similar to mammalian AQPs, water permeation of AgAQP1 is inhibited by HgCl2 and tetraethylammonium, with Tyr185 conferring tetraethylammonium sensitivity. AgAQP1 is more highly expressed in adult female A. gambiae mosquitoes than in males. Expression is high in gut, ovaries, and Malpighian tubules where immunofluorescence microscopy reveals that AgAQP1 resides in stellate cells but not principal cells. AgAQP1 expression is up-regulated in fat body and ovary by blood feeding but not by sugar feeding, and it is reduced by exposure to a dehydrating environment (42% relative humidity). RNA interference reduces AgAQP1 mRNA and protein levels. In a desiccating environment (<20% relative humidity), mosquitoes with reduced AgAQP1 protein survive significantly longer than controls. These studies support a role for AgAQP1 in water homeostasis during blood feeding and humidity adaptation of A. gambiae, a major mosquito vector of human malaria in sub-Saharan Africa. PMID:21444767

Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica.

PubMed

Guo, Yue; Liu, Jing; Zhang, Jiefu; Liu, Shengyi; Du, Jianchang

2017-07-01

It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories: positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (K a ) and the rates of synonymous substitution (K s ) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs. The resulting data show that PSGs have higher protein evolutionary rates, lower synonymous substitution rates, shorter gene length, fewer exons, higher functional specificity, lower expression level, higher tissue-specific expression and stronger codon bias than NSGs. Although the quantities and values are different, the relative features of PSGs and NSGs have been largely verified in the model species Arabidopsis. These data suggest that PSGs and NSGs differ not only under selective pressure (K a /K s ), but also in their evolutionary, structural and functional properties, indicating that selective modes may serve as a determinant factor for measuring evolutionary rates, gene compactness and expression patterns in Brassica. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Multiple Evolutionary Events Involved in Maintaining Homologs of Resistance to Powdery Mildew 8 in Brassica napus.

PubMed

Li, Qin; Li, Jing; Sun, Jin-Long; Ma, Xian-Feng; Wang, Ting-Ting; Berkey, Robert; Yang, Hui; Niu, Ying-Ze; Fan, Jing; Li, Yan; Xiao, Shunyuan; Wang, Wen-Ming

2016-01-01

The Resistance to Powdery Mildew 8 (RPW8) locus confers broad-spectrum resistance to powdery mildew in Arabidopsis thaliana. There are four Homologous to RPW8s (BrHRs) in Brassica rapa and three in Brassica oleracea (BoHRs). Brassica napus (Bn) is derived from diploidization of a hybrid between B. rapa and B. oleracea, thus should have seven homologs of RPW8 (BnHRs). It is unclear whether these genes are still maintained or lost in B. napus after diploidization and how they might have been evolved. Here, we reported the identification and sequence polymorphisms of BnHRs from a set of B. napus accessions. Our data indicated that while the BoHR copy from B. oleracea is highly conserved, the BrHR copy from B. rapa is relatively variable in the B. napus genome owing to multiple evolutionary events, such as gene loss, point mutation, insertion, deletion, and intragenic recombination. Given the overall high sequence homology of BnHR genes, it is not surprising that both intragenic recombination between two orthologs and two paralogs were detected in B. napus, which may explain the loss of BoHR genes in some B. napus accessions. When ectopically expressed in Arabidopsis, a C-terminally truncated version of BnHRa and BnHRb, as well as the full length BnHRd fused with YFP at their C-termini could trigger cell death in the absence of pathogens and enhanced resistance to powdery mildew disease. Moreover, subcellular localization analysis showed that both BnHRa-YFP and BnHRb-YFP were mainly localized to the extra-haustorial membrane encasing the haustorium of powdery mildew. Taken together, our data suggest that the duplicated BnHR genes might have been subjected to differential selection and at least some may play a role in defense and could serve as resistance resource in engineering disease-resistant plants.

Adaptation of New Colombian Food-based Complementary Feeding Recommendations Using Linear Programming.

PubMed

Tharrey, Marion; Olaya, Gilma A; Fewtrell, Mary; Ferguson, Elaine

2017-12-01

The aim of the study was to use linear programming (LP) analyses to adapt New Complementary Feeding Guidelines (NCFg) designed for infants aged 6 to 12 months living in poor socioeconomic circumstances in Bogota to ensure dietary adequacy for young children aged 12 to 23 months. A secondary data analysis was performed using dietary and anthropometric data collected from 12-month-old infants (n = 72) participating in a randomized controlled trial. LP analyses were performed to identify nutrients whose requirements were difficult to achieve using local foods as consumed; and to test and compare the NCFg and alternative food-based recommendations (FBRs) on the basis of dietary adequacy, for 11 micronutrients, at the population level. Thiamine recommended nutrient intakes for these young children could not be achieved given local foods as consumed. NCFg focusing only on meat, fruits, vegetables, and breast milk ensured dietary adequacy at the population level for only 4 micronutrients, increasing to 8 of 11 modelled micronutrients when the FBRs promoted legumes, dairy, vitamin A-rich vegetables, and chicken giblets. None of the FBRs tested ensured population-level dietary adequacy for thiamine, niacin, and iron unless a fortified infant food was recommended. The present study demonstrated the value of using LP to adapt NCFg for a different age group than the one for which they were designed. Our analyses suggest that to ensure dietary adequacy for 12- to 23-month olds these adaptations should include legumes, dairy products, vitamin A-rich vegetables, organ meat, and a fortified food.

Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

PubMed

Franks, Steven J; Kane, Nolan C; O'Hara, Niamh B; Tittes, Silas; Rest, Joshua S

2016-08-01

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome-wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late-season drought in California. These ancestor-descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (FST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome-wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Leaves play a central role in the adaptation of nitrogen and sulfur metabolism to ammonium nutrition in oilseed rape (Brassica napus).

PubMed

Coleto, Inmaculada; de la Peña, Marlon; Rodríguez-Escalante, Jon; Bejarano, Iraide; Glauser, Gaëtan; Aparicio-Tejo, Pedro M; González-Moro, M Begoña; Marino, Daniel

2017-09-20

The coordination between nitrogen (N) and sulfur (S) assimilation is required to suitably provide plants with organic compounds essential for their development and growth. The N source induces the adaptation of many metabolic processes in plants; however, there is scarce information about the influence that it may exert on the functioning of S metabolism. The aim of this work was to provide an overview of N and S metabolism in oilseed rape (Brassica napus) when exposed to different N sources. To do so, plants were grown in hydroponic conditions with nitrate or ammonium as N source at two concentrations (0.5 and 1 mM). Metabolic changes mainly occurred in leaves, where ammonium caused the up-regulation of enzymes involved in the primary assimilation of N and a general increase in the concentration of N-compounds (NH 4 + , amino acids and proteins). Similarly, the activity of key enzymes of primary S assimilation and the content of S-compounds (glutathione and glucosinolates) were also higher in leaves of ammonium-fed plants. Interestingly, sulfate level was lower in leaves of ammonium-fed plants, which was accompanied by the down-regulation of SULTR1 transporters gene expression. The results highlight the impact of the N source on different steps of N and S metabolism in oilseed rape, notably inducing N and S assimilation in leaves, and put forward the potential of N source management to modulate the synthesis of compounds with biotechnological interest, such as glucosinolates.

Which adaptive maternal eating behaviors predict child feeding practices? An examination with mothers of 2- to 5-year-old children

PubMed Central

Tylka, Tracy L.; Eneli, Ihuoma U.; Kroon Van Diest, Ashley M.; Lumeng, Julie C.

2013-01-01

Researchers have started to explore the detrimental impact of maladaptive maternal eating behaviors on child feeding practices. However, identifying which adaptive maternal eating behaviors contribute to lower use of negative and higher use of positive child feeding practices remains unexamined. The present study explored this link with 180 mothers of 2- to 5-year-old children. Hierarchical regression analyses (controlling for recruitment venue and maternal demographic characteristics, i.e., age, education, ethnicity, and body mass index) examined mothers’ intuitive eating and eating competence as predictors of four feeding practices (restriction, monitoring, pressure to eat, and dividing feeding responsibilities with their child). Mothers who gave themselves unconditional permission to eat were less likely to restrict their child’s food intake. Mothers who ate for physical (rather than emotional) reasons and had eating-related contextual skills (e.g., mindfulness when eating, planning regular and nutritious eating opportunities for themselves) were more likely to monitor their child’s food intake. Mothers who had eating-related contextual skills were more likely to divide feeding responsibilities with their child. No maternal eating behavior predicted pressure to eat. Interventions to help mothers develop their eating-related contextual skills and eat intuitively, in particular, may translate into a more positive feeding environment for their young children. PMID:23265403

Polyploidy and the relationship between leaf structure and function: implications for correlated evolution of anatomy, morphology, and physiology in Brassica.

PubMed

Baker, Robert L; Yarkhunova, Yulia; Vidal, Katherine; Ewers, Brent E; Weinig, Cynthia

2017-01-05

instability in early generation allotetraploids may allow Brassica species to explore new trait space and potentially reach higher adaptive peaks than their progenitor species could, despite temporary fitness costs associated with unstable genomes. The trait correlations that disappear after hybridization as well as the novel trait correlations observed in allotetraploid hybrids may represent relatively evolutionarily labile associations and therefore could be ideal targets for artificial selection and crop improvement.

Construction of Near Isogenic Lines in Brassica oleracea

USDA-ARS?s Scientific Manuscript database

The single species Brassica oleracea encompasses a remarkable diversity of morphotypes, including cauliflower, broccoli, kohlrabi, marrowstem kale, cabbage, and Brussels sprouts as well as rapid-flowering morphologically simple genotypes reminiscent of Arabidopsis. To dissect the molecular basis of ...

Nutritive quality and forage yield of three brassica varieties for use in livestock grazing systems

USDA-ARS?s Scientific Manuscript database

Brassicas are gaining popularity as high-quality forage for pasture-based livestock producers due to their use to extend the fall grazing season and during the summer forage slump. Little research has been conducted to evaluate forage yield and nutritive value of brassica species. A study was design...

Feeding of Diarmis Proboscis

ERIC Educational Resources Information Center

Young, Jocelyn

2005-01-01

The feeding of Diarmis proboscis is an exciting outdoor laboratory activity that demonstrates a single concept of adaptations--cryptic colorations. The students are "transformed" into D. proboscis (no Harry Potter magic needed) in order to learn how adaptations work in the natural world. Prior to beginning this activity, students should have a…

Genomic Analysis of Differentiation between Soil Types Reveals Candidate Genes for Local Adaptation in Arabidopsis lyrata

PubMed Central

Turner, Thomas L.; von Wettberg, Eric J.; Nuzhdin, Sergey V.

2008-01-01

Serpentine soil, which is naturally high in heavy metal content and has low calcium to magnesium ratios, comprises a difficult environment for most plants. An impressive number of species are endemic to serpentine, and a wide range of non-endemic plant taxa have been shown to be locally adapted to these soils. Locating genomic polymorphisms which are differentiated between serpentine and non-serpentine populations would provide candidate loci for serpentine adaptation. We have used the Arabidopsis thaliana tiling array, which has 2.85 million probes throughout the genome, to measure genetic differentiation between populations of Arabidopsis lyrata growing on granitic soils and those growing on serpentinic soils. The significant overrepresentation of genes involved in ion transport and other functions provides a starting point for investigating the molecular basis of adaptation to soil ion content, water retention, and other ecologically and economically important variables. One gene in particular, calcium-exchanger 7, appears to be an excellent candidate gene for adaptation to low Ca∶Mg ratio in A. lyrata. PMID:18784841

Differential expression and emerging functions of non-coding RNAs in cold adaptation.

PubMed

Frigault, Jacques J; Morin, Mathieu D; Morin, Pier Jr

2017-01-01

Several species undergo substantial physiological and biochemical changes to confront the harsh conditions associated with winter. Small mammalian hibernators and cold-hardy insects are examples of natural models of cold adaptation that have been amply explored. While the molecular picture associated with cold adaptation has started to become clearer in recent years, notably through the use of high-throughput experimental approaches, the underlying cold-associated functions attributed to several non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), remain to be better characterized. Nevertheless, key pioneering work has provided clues on the likely relevance of these molecules in cold adaptation. With an emphasis on mammalian hibernation and insect cold hardiness, this work first reviews various molecular changes documented so far in these processes. The cascades leading to miRNA and lncRNA production as well as the mechanisms of action of these non-coding RNAs are subsequently described. Finally, we present examples of differentially expressed non-coding RNAs in models of cold adaptation and elaborate on the potential significance of this modulation with respect to low-temperature adaptation.

Genome-Wide Identification and Characterization of Warming-Related Genes in Brassica rapa ssp. pekinensis.

PubMed

Song, Hayoung; Dong, Xiangshu; Yi, Hankuil; Ahn, Ju Young; Yun, Keunho; Song, Myungchul; Han, Ching-Tack; Hur, Yoonkang

2018-06-11

For sustainable crop cultivation in the face of global warming, it is important to unravel the genetic mechanisms underlying plant adaptation to a warming climate and apply this information to breeding. Thermomorphogenesis and ambient temperature signaling pathways have been well studied in model plants, but little information is available for vegetable crops. Here, we investigated genes responsive to warming conditions from two Brassica rapa inbred lines with different geographic origins: subtropical (Kenshin) and temperate (Chiifu). Genes in Gene Ontology categories “response to heat”, “heat acclimation”, “response to light intensity”, “response to oxidative stress”, and “response to temperature stimulus” were upregulated under warming treatment in both lines, but genes involved in “response to auxin stimulus” were upregulated only in Kenshin under both warming and minor-warming conditions. We identified 16 putative high temperature (HT) adaptation-related genes, including 10 heat-shock response genes, 2 transcription factor genes, 1 splicing factor gene, and 3 others. BrPIF4 , BrROF2 , and BrMPSR1 are candidate genes that might function in HT adaptation. Auxin response, alternative splicing of BrHSFA2 , and heat shock memory appear to be indispensable for HT adaptation in B. rapa . These results lay the foundation for molecular breeding and marker development to improve warming tolerance in B. rapa .

Consumption of a diet rich in Brassica vegetables is associated with a reduced abundance of sulphate-reducing bacteria: A randomised crossover study.

PubMed

Kellingray, Lee; Tapp, Henri S; Saha, Shikha; Doleman, Joanne F; Narbad, Arjan; Mithen, Richard F

2017-09-01

We examined whether a Brassica-rich diet was associated with an increase in the relative abundance of intestinal lactobacilli and sulphate-reducing bacteria (SRB), or alteration to the composition of the gut microbiota, in healthy adults. A randomised crossover study was performed with ten healthy adults who were fed a high- and a low-Brassica diet for 2-wk periods, with a 2-wk washout phase separating the diets. The high-Brassica diet consisted of six 84 g portions of broccoli, six 84 g portions of cauliflower and six 300 g portions of a broccoli and sweet potato soup. The low-Brassica diet consisted of one 84 g portion of broccoli and one 84 g portion of cauliflower. Faecal microbiota composition was measured in samples collected following 2-wk Brassica-free periods (consumption of all Brassica prohibited), and after each diet, whereby the only Brassica consumed was that supplied by the study team. No significant changes to the relative abundance of lactobacilli were observed (p = 0.8019). The increased consumption of Brassica was associated with a reduction in the relative abundance of SRB (p = 0.0215), and members of the Rikenellaceae, Ruminococcaceae, Mogibacteriaceae, Clostridium and unclassified Clostridiales (p < 0.01). The increased consumption of Brassica vegetables was linked to a reduced relative abundance of SRB, and therefore may be potentially beneficial to gastrointestinal health. © 2017 The Authors. Molecular Nutrition & Food Research published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The intensity of tyrosine nitration is associated with selenite and selenate toxicity in Brassica juncea L.

PubMed

Molnár, Árpád; Feigl, Gábor; Trifán, Vanda; Ördög, Attila; Szőllősi, Réka; Erdei, László; Kolbert, Zsuzsanna

2018-01-01

Selenium phytotoxicity involves processes like reactive nitrogen species overproduction and nitrosative protein modifications. This study evaluates the toxicity of two selenium forms (selenite and selenate at 0µM, 20µM, 50µM and 100µM concentrations) and its correlation with protein tyrosine nitration in the organs of hydroponically grown Indian mustard (Brassica juncea L.). Selenate treatment resulted in large selenium accumulation in both Brassica organs, while selenite showed slight root-to-shoot translocation resulting in a much lower selenium accumulation in the shoot. Shoot and root growth inhibition and cell viability loss revealed that Brassica tolerates selenate better than selenite. Results also show that relative high amounts of selenium are able to accumulate in Brassica leaves without obvious visible symptoms such as chlorosis or necrosis. The more severe phytotoxicity of selenite was accompanied by more intense protein tyrosine nitration as well as alterations in nitration pattern suggesting a correlation between the degree of Se forms-induced toxicities and nitroproteome size, composition in Brassica organs. These results imply the possibility of considering protein tyrosine nitration as novel biomarker of selenium phytotoxicity, which could help the evaluation of asymptomatic selenium stress of plants. Copyright © 2017 Elsevier Inc. All rights reserved.

A Genome-Wide Association Study Reveals New Loci for Resistance to Clubroot Disease in Brassica napus

PubMed Central

Li, Lixia; Luo, Yujie; Chen, Biyun; Xu, Kun; Zhang, Fugui; Li, Hao; Huang, Qian; Xiao, Xin; Zhang, Tianyao; Hu, Jihong; Li, Feng; Wu, Xiaoming

2016-01-01

Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. However, the yield and quality of rapeseed were largely decreased by clubroot (Plasmodiophora brassicae Woronin). Therefore, it is of great importance for screening more resistant germplasms or genes and improving the resistance to P. brassicae in rapeseed breeding. In this study, a massive resistant identification for a natural global population was conducted in two environments with race/pathotype 4 of P. brassicae which was the most predominant in China, and a wide range of phenotypic variation was found in the population. In addition, a genome-wide association study of 472 accessions for clubroot resistance (CR) was performed with 60K Brassica Infinium SNP arrays for the first time. In total, nine QTLs were detected, seven of which were novel through integrative analysis. Furthermore, additive effects in genetic control of CR in rapeseed among the above loci were found. By bioinformatic analyses, the candidate genes of these loci were predicted, which indicated that TIR-NBS gene family might play an important role in CR. It is believable that the results presented in our study could provide valuable information for understanding the genetic mechanism and molecular regulation of CR. PMID:27746804

Selection during crop diversification involves correlated evolution of the circadian clock and ecophysiological traits in Brassica rapa.

PubMed

Yarkhunova, Yulia; Edwards, Christine E; Ewers, Brent E; Baker, Robert L; Aston, Timothy Llewellyn; McClung, C Robertson; Lou, Ping; Weinig, Cynthia

2016-04-01

Crop selection often leads to dramatic morphological diversification, in which allocation to the harvestable component increases. Shifts in allocation are predicted to impact (as well as rely on) physiological traits; yet, little is known about the evolution of gas exchange and related anatomical features during crop diversification. In Brassica rapa, we tested for physiological differentiation among three crop morphotypes (leaf, turnip, and oilseed) and for correlated evolution of circadian, gas exchange, and phenological traits. We also examined internal and surficial leaf anatomical features and biochemical limits to photosynthesis. Crop types differed in gas exchange; oilseed varieties had higher net carbon assimilation and stomatal conductance relative to vegetable types. Phylogenetically independent contrasts indicated correlated evolution between circadian traits and both gas exchange and biomass accumulation; shifts to shorter circadian period (closer to 24 h) between phylogenetic nodes are associated with higher stomatal conductance, lower photosynthetic rate (when CO2 supply is factored out), and lower biomass accumulation. Crop type differences in gas exchange are also associated with stomatal density, epidermal thickness, numbers of palisade layers, and biochemical limits to photosynthesis. Brassica crop diversification involves correlated evolution of circadian and physiological traits, which is potentially relevant to understanding mechanistic targets for crop improvement. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Mouthpart conduit sizes of fluid-feeding insects determine the ability to feed from pores

DOE PAGES

Lehnert, Matthew S.; Bennett, Andrew; Reiter, Kristen E.; ...

2017-01-04

Fluid-feeding insects, such as butterflies, moths, and flies (20% of all animal species), are faced with the common selection pressure of having to remove and feed on trace amounts of fluids from porous surfaces. Insects able to acquire fluids that are confined to pores during drought conditions would have an adaptive advantage and increased fitness over other individuals. Here we performed feeding trials using solutions with magnetic nanoparticles to show that butterflies and flies have mouthparts adapted to pull liquids from porous surfaces using capillary action as the governing principle. In addition, the ability to feed on the liquids collectedmore » from pores depends on a relationship between the diameter of the mouthpart conduits and substrate pore size diameter; insects with mouthpart conduit diameters larger than the pores cannot successfully feed, thus there is a limiting substrate pore size from which each species can acquire liquids for fluid uptake. In conclusion, given that natural selection independently favored mouthpart architectures that support these methods of fluid uptake (Diptera and Lepidoptera share a common ancestor 280 mya that had chewing mouthparts), we suggest that the convergence of this mechanism advocates this as an optimal strategy for pulling trace amounts of fluids from porous surfaces.« less

Mouthpart conduit sizes of fluid-feeding insects determine the ability to feed from pores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehnert, Matthew S.; Bennett, Andrew; Reiter, Kristen E.

Fluid-feeding insects, such as butterflies, moths, and flies (20% of all animal species), are faced with the common selection pressure of having to remove and feed on trace amounts of fluids from porous surfaces. Insects able to acquire fluids that are confined to pores during drought conditions would have an adaptive advantage and increased fitness over other individuals. Here we performed feeding trials using solutions with magnetic nanoparticles to show that butterflies and flies have mouthparts adapted to pull liquids from porous surfaces using capillary action as the governing principle. In addition, the ability to feed on the liquids collectedmore » from pores depends on a relationship between the diameter of the mouthpart conduits and substrate pore size diameter; insects with mouthpart conduit diameters larger than the pores cannot successfully feed, thus there is a limiting substrate pore size from which each species can acquire liquids for fluid uptake. In conclusion, given that natural selection independently favored mouthpart architectures that support these methods of fluid uptake (Diptera and Lepidoptera share a common ancestor 280 mya that had chewing mouthparts), we suggest that the convergence of this mechanism advocates this as an optimal strategy for pulling trace amounts of fluids from porous surfaces.« less

Pollination and embryo development in Brassica rapa L. in microgravity

NASA Technical Reports Server (NTRS)

Kuang, A.; Popova, A.; Xiao, Y.; Musgrave, M. E.

2000-01-01

Plant reproduction under spaceflight conditions has been problematic in the past. In order to determine what aspect of reproductive development is affected by microgravity, we studied pollination and embryo development in Brassica rapa L. during 16 d in microgravity on the space shuttle (STS-87). Brassica is self-incompatible and requires mechanical transfer of pollen. Short-duration access to microgravity during parabolic flights on the KC-135A aircraft was used initially to confirm that equal numbers of pollen grains could be collected and transferred in the absence of gravity. Brassica was grown in the Plant Growth Facility flight hardware as follows. Three chambers each contained six plants that were 13 d old at launch. As these plants flowered, thin colored tape was used to indicate the date of hand pollination, resulting in silique populations aged 8-15 d postpollination at the end of the 16-d mission. The remaining three chambers contained dry seeds that germinated on orbit to produce 14-d-old plants just beginning to flower at the time of landing. Pollen produced by these plants had comparable viability (93%) with that produced in the 2-d-delayed ground control. Matched-age siliques yielded embryos of equivalent developmental stage in the spaceflight and ground control treatments. Carbohydrate and protein storage reserves in the embryos, assessed by cytochemical localization, were also comparable. In the spaceflight material, growth and development by embryos rescued from siliques 15 d after pollination lagged behind the ground controls by 12 d; however, in the subsequent generation, no differences between the two treatments were found. The results demonstrate that while no stage of reproductive development in Brassica is absolutely dependent upon gravity, lower embryo quality may result following development in microgravity.

Evidence of correlated evolution and adaptive differentiation of stem and leaf functional traits in the herbaceous genus, Helianthus.

PubMed

Pilote, Alex J; Donovan, Lisa A

2016-12-01

Patterns of plant stem traits are expected to align with a "fast-slow" plant economic spectrum across taxa. Although broad patterns support such tradeoffs in field studies, tests of hypothesized correlated trait evolution and adaptive differentiation are more robust when taxa relatedness and environment are taken into consideration. Here we test for correlated evolution of stem and leaf traits and their adaptive differentiation across environments in the herbaceous genus, Helianthus. Stem and leaf traits of 14 species of Helianthus (28 populations) were assessed in a common garden greenhouse study. Phylogenetically independent contrasts were used to test for evidence of correlated evolution of stem hydraulic and biomechanical properties, correlated evolution of stem and leaf traits, and adaptive differentiation associated with source habitat environments. Among stem traits, there was evidence for correlated evolution of some hydraulic and biomechanical properties, supporting an expected tradeoff between stem theoretical hydraulic efficiency and resistance to bending stress. Population differentiation for suites of stem and leaf traits was found to be consistent with a "fast-slow" resource-use axis for traits related to water transport and use. Associations of population traits with source habitat characteristics supported repeated evolution of a resource-acquisitive "drought-escape" strategy in arid environments. This study provides evidence of correlated evolution of stem and leaf traits consistent with the fast-slow spectrum of trait combinations related to water transport and use along the stem-to-leaf pathway. Correlations of traits with source habitat characteristics further indicate that the correlated evolution is associated, at least in part, with adaptive differentiation of Helianthus populations among native habitats differing in climate. © 2016 Botanical Society of America.

Destiny of a transgene escape from Brassica napus into Brassica rapa.

PubMed

Lu, M.; Kato, M.; Kakihara, F.

2002-07-01

Transgenic Brassica napus can be easily crossed with wild Brassica rapa. The spread of the transgene to wild species has aroused the general concern about its effect on ecological and agricultural systems. This paper was designated, by means of population genetics, to study the fate of a transgene escape from B. napus to B. rapa. Three models were proposed to survey the change in gene frequency during successive backcross processes by considering selection pressures against aneuploids, against herbicide-susceptible individuals, and by considering A-C intergenomic recombination and the effect of genetic drift. The transmission rate of an A-chromosome gene through an individual to the next generation was 50%, irrespective of the chromosome number; while that of a C-chromosome transgene varied from 8.7% to 39.9%, depending on the chromosome number of the individual used in the backcross. Without spraying herbicide, the frequency of an A-chromosome gene was 50% in the BC(1) generation, and decreased by 50% with the advance of each backcross generation; that of a C-chromosome gene was around 39.9% in BC(1), 7.7% in BC(2), 1.2% in BC(3) and 0.1% in the BC(4) generation. Under the selection pressure against herbicide-susceptible individuals, the frequency of a transgene reached a stable value of about 5.5% within six generations of successive backcrossings. The effect of genetic drift and intergenomic exchange on gene transmission rate was discussed. It is suggested that the transgene integrated on a C-chromosome (or better on a cytoplasm genome) is safer than that on an A-chromosome. The transgenic cultivars should be cultivated rotationally by year(s) with other non-transgenic varieties in order to reduce the transfer of the transgene to wild B. rapa species.

Service differentiated and adaptive CSMA/CA over IEEE 802.15.4 for Cyber-Physical Systems.

PubMed

Xia, Feng; Li, Jie; Hao, Ruonan; Kong, Xiangjie; Gao, Ruixia

2013-01-01

Cyber-Physical Systems (CPS) that collect, exchange, manage information, and coordinate actions are an integral part of the Smart Grid. In addition, Quality of Service (QoS) provisioning in CPS, especially in the wireless sensor/actuator networks, plays an essential role in Smart Grid applications. IEEE 802.15.4, which is one of the most widely used communication protocols in this area, still needs to be improved to meet multiple QoS requirements. This is because IEEE 802.15.4 slotted Carrier Sense Multiple Access/Collision Avoidance (CSMA/CA) employs static parameter configuration without supporting differentiated services and network self-adaptivity. To address this issue, this paper proposes a priority-based Service Differentiated and Adaptive CSMA/CA (SDA-CSMA/CA) algorithm to provide differentiated QoS for various Smart Grid applications as well as dynamically initialize backoff exponent according to traffic conditions. Simulation results demonstrate that the proposed SDA-CSMA/CA scheme significantly outperforms the IEEE 802.15.4 slotted CSMA/CA in terms of effective data rate, packet loss rate, and average delay.

Service Differentiated and Adaptive CSMA/CA over IEEE 802.15.4 for Cyber-Physical Systems

PubMed Central

Gao, Ruixia

2013-01-01

Cyber-Physical Systems (CPS) that collect, exchange, manage information, and coordinate actions are an integral part of the Smart Grid. In addition, Quality of Service (QoS) provisioning in CPS, especially in the wireless sensor/actuator networks, plays an essential role in Smart Grid applications. IEEE 802.15.4, which is one of the most widely used communication protocols in this area, still needs to be improved to meet multiple QoS requirements. This is because IEEE 802.15.4 slotted Carrier Sense Multiple Access/Collision Avoidance (CSMA/CA) employs static parameter configuration without supporting differentiated services and network self-adaptivity. To address this issue, this paper proposes a priority-based Service Differentiated and Adaptive CSMA/CA (SDA-CSMA/CA) algorithm to provide differentiated QoS for various Smart Grid applications as well as dynamically initialize backoff exponent according to traffic conditions. Simulation results demonstrate that the proposed SDA-CSMA/CA scheme significantly outperforms the IEEE 802.15.4 slotted CSMA/CA in terms of effective data rate, packet loss rate, and average delay. PMID:24260021

The Brassica epithionitrile 1-cyano-2,3-epithiopropane triggers cell death in human liver cancer cells in vitro.

PubMed

Hanschen, Franziska S; Herz, Corinna; Schlotz, Nina; Kupke, Franziska; Bartolomé Rodríguez, María M; Schreiner, Monika; Rohn, Sascha; Lamy, Evelyn

2015-11-01

Glucosinolates are secondary metabolites present in Brassica vegetables. Alkenyl glucosinolates are enzymatically degraded forming nitriles or isothiocyanates, but in the presence of epithiospecifier protein, epithionitriles are released. However, studies on the occurrence of epithionitriles in Brassica food and knowledge about their biological effects are scarce. Epithionitrile formation from glucosinolates of seven Brassica vegetables was analyzed using GC-MS and HPLC-DAD. Bioactivity of synthetic and plant-derived 1-cyano-2,3-epithiopropane (CETP) - the predominant epithionitrile in Brassica vegetables - in three human hepatocellular carcinoma (HCC) cell lines and primary murine hepatocytes was also evaluated. The majority of the Brassica vegetables were producers of nitriles or epithionitriles as hydrolysis products and not of isothiocyanates. For example, Brussels sprouts and savoy cabbage contained up to 0.8 μmol CETP/g vegetable. Using formazan dye assays, concentrations of 380-1500 nM CETP were observed to inhibit the mitochondrial dehydrogenase activity of human HCC cells without impairment of cell growth. At 100-fold higher CETP concentrations, cell death was observed. Presence of plant matrix increased CETP-based toxicity. These in vitro data provide no indication that epithionitriles will severely affect human health by Brassica consumption. In contrast to isothiocyanates, no evidence of selective toxicity against HCC cells was found. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of a new high copy Stowaway family MITE, BRAMI-1 in Brassica genome

PubMed Central

2013-01-01

Background Miniature inverted-repeat transposable elements (MITEs) are expected to play important roles in evolution of genes and genome in plants, especially in the highly duplicated plant genomes. Various MITE families and their roles in plants have been characterized. However, there have been fewer studies of MITE families and their potential roles in evolution of the recently triplicated Brassica genome. Results We identified a new MITE family, BRAMI-1, belonging to the Stowaway super-family in the Brassica genome. In silico mapping revealed that 697 members are dispersed throughout the euchromatic regions of the B. rapa pseudo-chromosomes. Among them, 548 members (78.6%) are located in gene-rich regions, less than 3 kb from genes. In addition, we identified 516 and 15 members in the 470 Mb and 15 Mb genomic shotgun sequences currently available for B. oleracea and B. napus, respectively. The resulting estimated copy numbers for the entire genomes were 1440, 1464 and 2490 in B. rapa, B. oleracea and B. napus, respectively. Concurrently, only 70 members of the related Arabidopsis ATTIRTA-1 MITE family were identified in the Arabidopsis genome. Phylogenetic analysis revealed that BRAMI-1 elements proliferated in the Brassica genus after divergence from the Arabidopsis lineage. MITE insertion polymorphism (MIP) was inspected for 50 BRAMI-1 members, revealing high levels of insertion polymorphism between and within species of Brassica that clarify BRAMI-1 activation periods up to the present. Comparative analysis of the 71 genes harbouring the BRAMI-1 elements with their non-insertion paralogs (NIPs) showed that the BRAMI-1 insertions mainly reside in non-coding sequences and that the expression levels of genes with the elements differ from those of their NIPs. Conclusion A Stowaway family MITE, named as BRAMI-1, was gradually amplified and remained present in over than 1400 copies in each of three Brassica species. Overall, 78% of the members were identified in

Relationship of Enhanced Butyrate Production by Colonic Butyrate-Producing Bacteria to Immunomodulatory Effects in Normal Mice Fed an Insoluble Fraction of Brassica rapa L.

PubMed Central

Tanaka, Sachi; Yamamoto, Kana; Yamada, Kazuki; Furuya, Kanon

2016-01-01

This study was performed to determine the effects of feeding a fiber-rich fraction of Brassica vegetables on the immune response through changes in enteric bacteria and short-chain fatty acid (SCFA) production in normal mice. The boiled-water-insoluble fraction of Brassica rapa L. (nozawana), which consists mainly of dietary fiber, was chosen as a test material. A total of 31 male C57BL/6J mice were divided into two groups and housed in a specific-pathogen-free facility. The animals were fed either a control diet or the control diet plus the insoluble B. rapa L. fraction for 2 weeks and sacrificed to determine microbiological and SCFA profiles in lower-gut samples and immunological molecules. rRNA-based quantification indicated that the relative population of Bacteroidetes was markedly lower in the colon samples of the insoluble B. rapa L. fraction-fed group than that in the controls. Populations of the Eubacterium rectale group and Faecalibacterium prausnitzii, both of which are representative butyrate-producing bacteria, doubled after 2 weeks of fraction intake, accompanying a marginal increase in the proportion of colonic butyrate. In addition, feeding with the fraction significantly increased levels of the anti-inflammatory cytokine interleukin-10 (IL-10) and tended to increase splenic regulatory T cell numbers but significantly reduced the population of cells expressing activation markers. We demonstrated that inclusion of the boiled-water-insoluble fraction of B. rapa L. can alter the composition of the gut microbiota to decrease the numbers of Bacteroidetes and to increase the numbers of butyrate-producing bacteria, either of which may be involved in the observed shift in the production of splenic IL-10. PMID:26921420

Application of the Modular Automated Reconfigurable Assembly System (MARAS) concept to adaptable vision gauging and parts feeding

NASA Technical Reports Server (NTRS)

By, Andre Bernard; Caron, Ken; Rothenberg, Michael; Sales, Vic

1994-01-01

This paper presents the first phase results of a collaborative effort between university researchers and a flexible assembly systems integrator to implement a comprehensive modular approach to flexible assembly automation. This approach, named MARAS (Modular Automated Reconfigurable Assembly System), has been structured to support multiple levels of modularity in terms of both physical components and system control functions. The initial focus of the MARAS development has been on parts gauging and feeding operations for cylinder lock assembly. This phase is nearing completion and has resulted in the development of a highly configurable system for vision gauging functions on a wide range of small components (2 mm to 100 mm in size). The reconfigurable concepts implemented in this adaptive Vision Gauging Module (VGM) are now being extended to applicable aspects of the singulating, selecting, and orienting functions required for the flexible feeding of similar mechanical components and assemblies.

Proteomic Dissection of Seed Germination and Seedling Establishment in Brassica napus

PubMed Central

Gu, Jianwei; Chao, Hongbo; Gan, Lu; Guo, Liangxing; Zhang, Kai; Li, Yonghong; Wang, Hao; Raboanatahiry, Nadia; Li, Maoteng

2016-01-01

The success of seed germination and establishment of a normal seedling are key determinants of plant species propagation. At present, only a few studies have focused on the genetic control of seed germination by using a proteomic approach in Brassica napus. In the present study, the protein expression pattern of seed germination was investigated using differential fluorescence two-dimensional gel electrophoresis in B. napus. One hundred and thirteen differentially expressed proteins (DEPs) that were mainly involved in storage (23.4%), energy metabolism (18.9%), protein metabolism (16.2%), defense/disease (12.6%), seed maturation (11.7%), carbohydrate metabolism (4.5%), lipid metabolism (4.5%), amino acids metabolism (3.6%), cell growth/division (3.6%), and some unclear functions (2.7%) were observed by proteomic analysis. Seventeen genes corresponding to 11 DEPs were identified within or near the associated linkage disequilibrium regions related to seed germination and vigor quantitative traits reported in B. napus in previous studies. The expression pattern of proteins showed that heterotrophic metabolism could be activated in the process of seed germination and that the onset of defense mechanisms might start during seed germination. These findings will help generate a more in-depth understanding of the mobilization of seed storage reserves and regulation mechanisms of the germination process in B. napus. PMID:27822216

Phosphate-assisted phytoremediation of arsenic by Brassica napus and Brassica juncea: Morphological and physiological response.

PubMed

Niazi, Nabeel Khan; Bibi, Irshad; Fatimah, Ayesha; Shahid, Muhammad; Javed, Muhammad Tariq; Wang, Hailong; Ok, Yong Sik; Bashir, Safdar; Murtaza, Behzad; Saqib, Zulfiqar Ahmad; Shakoor, Muhammad Bilal

2017-07-03

In this study, we examined the potential role of phosphate (P; 0, 50, 100 mg kg -1 ) on growth, gas exchange attributes, and photosynthetic pigments of Brassica napus and Brassica juncea under arsenic (As) stress (0, 25, 50, 75 mg kg -1 ) in a pot experiment. Results revealed that phosphate supplementation (P100) to As-stressed plants significantly increased shoot As concentration, dry biomass yield, and As uptake, in addition to the improved morphological and gas exchange attributes and photosynthetic pigments over P0. However, phosphate-assisted increase in As uptake was substantially (up to two times) greater for B. napus, notably due to higher shoot As concentration and dry biomass yield, compared to B. juncea at the P100 level. While phosphate addition in soil (P100) led to enhanced shoot As concentration in B. juncea, it reduced shoot dry biomass, primarily after 50 and 75 mg kg -1 As treatments. The translocation factor and bioconcentration factor values of B. napus were higher than B. juncea for all As levels in the presence of phosphate. This study demonstrates that phosphate supplementation has a potential to improve As phytoextraction efficiency, predominantly for B. napus, by minimizing As-induced damage to plant growth, as well as by improving the physiological and photosynthetic attributes.

Comparative quantitative trait loci for silique length and seed weight in Brassica napus.

PubMed

Fu, Ying; Wei, Dayong; Dong, Hongli; He, Yajun; Cui, Yixin; Mei, Jiaqin; Wan, Huafang; Li, Jiana; Snowdon, Rod; Friedt, Wolfgang; Li, Xiaorong; Qian, Wei

2015-09-23

Silique length (SL) and seed weight (SW) are important yield-associated traits in rapeseed (Brassica napus). Although many quantitative trait loci (QTL) for SL and SW have been identified in B. napus, comparative analysis for those QTL is seldom performed. In the present study, 20 and 21 QTL for SL and SW were identified in doubled haploid (DH) and DH-derived reconstructed F2 populations in rapeseed, explaining 55.1-74.3% and 24.4-62.9% of the phenotypic variation across three years, respectively. Of which, 17 QTL with partially or completely overlapped confidence interval on chromosome A09, were homologous with two overlapped QTL on chromosome C08 by aligning QTL confidence intervals with the reference genomes of Brassica crops. By high density selective genotyping of DH lines with extreme phenotypes, using a Brassica single-nucleotide polymorphism (SNP) array, the QTL on chromosome A09 was narrowed, and aligned into 1.14-Mb region from 30.84 to 31.98 Mb on chromosome R09 of B. rapa and 1.05-Mb region from 27.21 to 28.26 Mb on chromosome A09 of B. napus. The alignment of QTL with Brassica reference genomes revealed homologous QTL on A09 and C08 for SL. The narrowed QTL region provides clues for gene cloning and breeding cultivars by marker-assisted selection.

Phytotoxicity evaluation of some commonly used shampoos using Brassica napus L.

PubMed

Naeem, Faiqa; Ahmed, Faiza; Kanwal, Memoona; Murad, Waheed; Azizullah, Azizullah

2015-10-01

Hair shampoos are among the most commonly used chemicals in everyday life. Since shampoos are a major component of domestic and municipal wastewater, they may affect plants when irrigated with wastewater. However, their effects on plants have never been investigated in detail. The present study was aimed to evaluate the effect of some commonly used hair shampoos on seed germination and seedling vigor of Brassica napus. Seeds of Brassica napus were exposed to different concentrations of hair shampoos, i.e., 0 (control), 0.001, 0.01, 0.1, 1.0, and 10 %. The obtained results revealed that germination was not very sensitive to shampoo stress and was significantly inhibited only at the highest tested concentration (10 %) of shampoo except in the case of one shampoo where it was inhibited at concentration of 1 % or above. The other tested parameters of Brassica napus were comparatively more sensitive than germination to shampoo stress. However, at lower concentrations of shampoos, stimulatory effects were also observed in some cases. Although no exact data is available on shampoo concentration in wastewater used for irrigation, it is unlikely that shampoo concentration in irrigation water reach so high and pose adversity to plants.

Phenotyping of Brassica napus for high oil content

USDA-ARS?s Scientific Manuscript database

Multi-trait and multi-growth stage phenotyping may improve our ability to assess the dynamic changes in the B. napus phenome under spatiotemporal field conditions. A minimum set of phenotypic traits that can integrate ontogeny and architecture of Brassica napus L. is required for breeding and select...

ADAPTIVE METHODS FOR STOCHASTIC DIFFERENTIAL EQUATIONS VIA NATURAL EMBEDDINGS AND REJECTION SAMPLING WITH MEMORY.

PubMed

Rackauckas, Christopher; Nie, Qing

2017-01-01

Adaptive time-stepping with high-order embedded Runge-Kutta pairs and rejection sampling provides efficient approaches for solving differential equations. While many such methods exist for solving deterministic systems, little progress has been made for stochastic variants. One challenge in developing adaptive methods for stochastic differential equations (SDEs) is the construction of embedded schemes with direct error estimates. We present a new class of embedded stochastic Runge-Kutta (SRK) methods with strong order 1.5 which have a natural embedding of strong order 1.0 methods. This allows for the derivation of an error estimate which requires no additional function evaluations. Next we derive a general method to reject the time steps without losing information about the future Brownian path termed Rejection Sampling with Memory (RSwM). This method utilizes a stack data structure to do rejection sampling, costing only a few floating point calculations. We show numerically that the methods generate statistically-correct and tolerance-controlled solutions. Lastly, we show that this form of adaptivity can be applied to systems of equations, and demonstrate that it solves a stiff biological model 12.28x faster than common fixed timestep algorithms. Our approach only requires the solution to a bridging problem and thus lends itself to natural generalizations beyond SDEs.

ADAPTIVE METHODS FOR STOCHASTIC DIFFERENTIAL EQUATIONS VIA NATURAL EMBEDDINGS AND REJECTION SAMPLING WITH MEMORY

PubMed Central

Rackauckas, Christopher

2017-01-01

Adaptive time-stepping with high-order embedded Runge-Kutta pairs and rejection sampling provides efficient approaches for solving differential equations. While many such methods exist for solving deterministic systems, little progress has been made for stochastic variants. One challenge in developing adaptive methods for stochastic differential equations (SDEs) is the construction of embedded schemes with direct error estimates. We present a new class of embedded stochastic Runge-Kutta (SRK) methods with strong order 1.5 which have a natural embedding of strong order 1.0 methods. This allows for the derivation of an error estimate which requires no additional function evaluations. Next we derive a general method to reject the time steps without losing information about the future Brownian path termed Rejection Sampling with Memory (RSwM). This method utilizes a stack data structure to do rejection sampling, costing only a few floating point calculations. We show numerically that the methods generate statistically-correct and tolerance-controlled solutions. Lastly, we show that this form of adaptivity can be applied to systems of equations, and demonstrate that it solves a stiff biological model 12.28x faster than common fixed timestep algorithms. Our approach only requires the solution to a bridging problem and thus lends itself to natural generalizations beyond SDEs. PMID:29527134

Wounding, insect chewing and phloem sap feeding differentially alter the leaf proteome of potato, Solanum tuberosum L.

PubMed Central

2012-01-01

Background Various factors shape the response of plants to herbivorous insects, including wounding patterns, specific chemical effectors and feeding habits of the attacking herbivore. Here we performed a comparative proteomic analysis of the plant's response to wounding and herbivory, using as a model potato plants (Solanum tuberosum L.) subjected to mechanical wounding, defoliation by the Colorado potato beetle Leptinotarsa decemlineata Say, or phloem sap feeding by the potato aphid Macrosiphum euphorbiae Thomas. Results Out of ~500 leaf proteins monitored by two-dimensional gel electrophoresis (2-DE), 31 were up- or downregulated by at least one stress treatment compared to healthy control plants. Of these proteins, 29 were regulated by beetle chewing, 8 by wounding and 8 by aphid feeding. Some proteins were up- or downregulated by two different treatments, while others showed diverging expression patterns in response to different treatments. A number of modulated proteins identified by mass spectrometry were typical defense proteins, including wound-inducible protease inhibitors and pathogenesis-related proteins. Proteins involved in photosynthesis were also modulated, notably by potato beetle feeding inducing a strong decrease of some photosystem I proteins. Quantitative RT PCR assays were performed with nucleotide primers for photosynthesis-related proteins to assess the impact of wounding and herbivory at the gene level. Whereas different, sometimes divergent, responses were observed at the proteome level in response to wounding and potato beetle feeding, downregulating effects were systematically observed for both treatments at the transcriptional level. Conclusions These observations illustrate the differential impacts of wounding and insect herbivory on defense- and photosynthesis-related components of the potato leaf proteome, likely associated with the perception of distinct physical and chemical cues in planta. PMID:23268880

Genomic evidence for genes encoding leucine-rich repeat receptors linked to resistance against the eukaryotic extra- and intracellular Brassica napus pathogens Leptosphaeria maculans and Plasmodiophora brassicae.

PubMed

Stotz, Henrik U; Harvey, Pascoe J; Haddadi, Parham; Mashanova, Alla; Kukol, Andreas; Larkan, Nicholas J; Borhan, M Hossein; Fitt, Bruce D L

2018-01-01

Genes coding for nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) control resistance against intracellular (cell-penetrating) pathogens. However, evidence for a role of genes coding for proteins with LRR domains in resistance against extracellular (apoplastic) fungal pathogens is limited. Here, the distribution of genes coding for proteins with eLRR domains but lacking kinase domains was determined for the Brassica napus genome. Predictions of signal peptide and transmembrane regions divided these genes into 184 coding for receptor-like proteins (RLPs) and 121 coding for secreted proteins (SPs). Together with previously annotated NLRs, a total of 720 LRR genes were found. Leptosphaeria maculans-induced expression during a compatible interaction with cultivar Topas differed between RLP, SP and NLR gene families; NLR genes were induced relatively late, during the necrotrophic phase of pathogen colonization. Seven RLP, one SP and two NLR genes were found in Rlm1 and Rlm3/Rlm4/Rlm7/Rlm9 loci for resistance against L. maculans on chromosome A07 of B. napus. One NLR gene at the Rlm9 locus was positively selected, as was the RLP gene on chromosome A10 with LepR3 and Rlm2 alleles conferring resistance against L. maculans races with corresponding effectors AvrLm1 and AvrLm2, respectively. Known loci for resistance against L. maculans (extracellular hemi-biotrophic fungus), Sclerotinia sclerotiorum (necrotrophic fungus) and Plasmodiophora brassicae (intracellular, obligate biotrophic protist) were examined for presence of RLPs, SPs and NLRs in these regions. Whereas loci for resistance against P. brassicae were enriched for NLRs, no such signature was observed for the other pathogens. These findings demonstrate involvement of (i) NLR genes in resistance against the intracellular pathogen P. brassicae and a putative NLR gene in Rlm9-mediated resistance against the extracellular pathogen L. maculans.

Increasing self-drinking for children with feeding disorders.

PubMed

Peterson, Kathryn M; Volkert, Valerie M; Zeleny, Jason R

2015-01-01

Children with feeding disorders often do not self-drink without treatment. Unfortunately, the literature on self-drinking is scarce. We evaluated differential positive reinforcement to increase self-drinking for 2 children with feeding disorders. Results showed that differential positive reinforcement with tangible items increased self-drinking for both children in the absence of nonremoval of the cup. © Society for the Experimental Analysis of Behavior.

Basis adaptation and domain decomposition for steady partial differential equations with random coefficients

DOE PAGES

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

2017-09-04

In this paper, we present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support ourmore » construction with numerical experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Lastly, our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.« less

Neofunctionalization of duplicated Tic40 genes caused a gain-of-function variation related to male fertility in Brassica oleracea lineages.

PubMed

Dun, Xiaoling; Shen, Wenhao; Hu, Kaining; Zhou, Zhengfu; Xia, Shengqian; Wen, Jing; Yi, Bin; Shen, Jinxiong; Ma, Chaozhi; Tu, Jinxing; Fu, Tingdong; Lagercrantz, Ulf

2014-11-01

Gene duplication followed by functional divergence in the event of polyploidization is a major contributor to evolutionary novelties. The Brassica genus evolved from a common ancestor after whole-genome triplication. Here, we studied the evolutionary and functional features of Brassica spp. homologs to Tic40 (for translocon at the inner membrane of chloroplasts with 40 kDa). Four Tic40 loci were identified in allotetraploid Brassica napus and two loci in each of three basic diploid Brassica spp. Although these Tic40 homologs share high sequence identities and similar expression patterns, they exhibit altered functional features. Complementation assays conducted on Arabidopsis thaliana tic40 and the B. napus male-sterile line 7365A suggested that all Brassica spp. Tic40 homologs retain an ancestral function similar to that of AtTic40, whereas BolC9.Tic40 in Brassica oleracea and its ortholog in B. napus, BnaC9.Tic40, in addition, evolved a novel function that can rescue the fertility of 7365A. A homologous chromosomal rearrangement placed bnac9.tic40 originating from the A genome (BraA10.Tic40) as an allele of BnaC9.Tic40 in the C genome, resulting in phenotypic variation for male sterility in the B. napus near-isogenic two-type line 7365AB. Assessment of the complementation activity of chimeric B. napus Tic40 domain-swapping constructs in 7365A suggested that amino acid replacements in the carboxyl terminus of BnaC9.Tic40 cause this functional divergence. The distribution of these amino acid replacements in 59 diverse Brassica spp. accessions demonstrated that the neofunctionalization of Tic40 is restricted to B. oleracea and its derivatives and thus occurred after the divergence of the Brassica spp. A, B, and C genomes. © 2014 American Society of Plant Biologists. All Rights Reserved.

Genetic and morphological data supporting the hypothesis of adaptive radiation in the endemic fish of Lake Matano.

PubMed

Roy, D; Docker, M F; Hehanussa, P; Heath, D D; Haffner, G D

2004-11-01

Adaptive radiation resulting from differential selection acting on functional features is believed to be an important source of biodiversity. In this study, morphometric measures and mitochondrial DNA are used to test for adaptive radiation within four fish genera (Glossogobius, Oryzias, Dermogenys and Telmatherina) endemic to an ancient island lake (Lake Matano, Sulawesi, Indonesia), using the framework proposed by Schluter (The Ecology of Adaptive Radiation, Oxford University Press, 2000). We demonstrate common ancestry and rapid divergence in one genus (Telmatherina) based on 560 bp of 16S sequence data. We found higher levels of variation in feeding-related traits (N = 8) for Telmatherina relative to the other genera, while no differences were found for sexual display traits (N = 8) or neutral morphological traits (N = 8). Telmatherina also had the highest number of distinct colouration patterns among the four genera. These data, combined with the very low productivity of the lake, are indicative of selection driving adaptive radiation. The morphometric divergence in the Telmatherina likely results from selection acting on feeding traits in this low productivity lake, leading to trophic specialization among closely related morphotypes. These results provide indirect but compelling data supporting the adaptive radiation of Telmatherina in this system.

Practices and health perception of preparation of Brassica vegetables: translating survey data to technological and nutritional implications.

PubMed

Nugrahedi, Probo Y; Hantoro, Inneke; Verkerk, Ruud; Dekker, Matthijs; Steenbekkers, Bea

2015-01-01

Food preparation practices are known to have large nutritional implications on the final product. This article describes survey data on preparation practices of Brassica vegetables and the translation of these data into technological and nutritional implications using knowledge on the mechanisms of changes in the content of phytochemicals. The survey on preparation practices was performed with food service establishments (n = 123) and households (n = 477) in Semarang, Indonesia, and assessed the food handlers' perception of the health benefits of these vegetables. Boiling and stir-frying are the most frequently applied techniques to prepare Brassicas. The respondents perceive that steaming, boiling, and stir-frying result in vegetables with a high health benefit. White cabbage and choysum are the most frequently prepared Brassicas. However, broccoli is perceived as the healthiest. The consequences of the various applied preparation techniques on the content of alleged health promoting phytochemicals (glucosinolates) in dishes containing Brassica vegetables are discussed.

Oviposition Preference for Young Plants by the Large Cabbage Butterfly (Pieris brassicae ) Does not Strongly Correlate with Caterpillar Performance.

PubMed

Fei, Minghui; Harvey, Jeffrey A; Yin, Yi; Gols, Rieta

2017-06-01

The effects of temporal variation in the quality of short-lived annual plants on oviposition preference and larval performance of insect herbivores has thus far received little attention. This study examines the effects of plant age on female oviposition preference and offspring performance in the large cabbage white butterfly Pieris brassicae. Adult female butterflies lay variable clusters of eggs on the underside of short-lived annual species in the family Brassicaceae, including the short-lived annuals Brassica nigra and Sinapis arvensis, which are important food plants for P. brassicae in The Netherlands. Here, we compared oviposition preference and larval performance of P. brassicae on three age classes (young, mature, and pre-senescing) of B. nigra and S. arvensis plants. Oviposition preference of P. brassicae declined with plant age in both plant species. Whereas larvae performed similarly on all three age classes in B. nigra, preference and performance were weakly correlated in S. arvensis. Analysis of primary (sugars and amino acids) and secondary (glucosinolates) chemistry in the plant shoots revealed that differences in their quality and quantity were more pronounced with respect to tissue type (leaves vs. flowers) than among different developmental stages of both plant species. Butterflies of P. brassicae may prefer younger and smaller plants for oviposition anticipating that future plant growth and size is optimally synchronized with the final larval instar, which contributes >80% of larval growth before pupation.

Transposon variation by order during allopolyploidisation between Brassica oleracea and Brassica rapa.

PubMed

An, Z; Tang, Z; Ma, B; Mason, A S; Guo, Y; Yin, J; Gao, C; Wei, L; Li, J; Fu, D

2014-07-01

Although many studies have shown that transposable element (TE) activation is induced by hybridisation and polyploidisation in plants, much less is known on how different types of TE respond to hybridisation, and the impact of TE-associated sequences on gene function. We investigated the frequency and regularity of putative transposon activation for different types of TE, and determined the impact of TE-associated sequence variation on the genome during allopolyploidisation. We designed different types of TE primers and adopted the Inter-Retrotransposon Amplified Polymorphism (IRAP) method to detect variation in TE-associated sequences during the process of allopolyploidisation between Brassica rapa (AA) and Brassica oleracea (CC), and in successive generations of self-pollinated progeny. In addition, fragments with TE insertions were used to perform Blast2GO analysis to characterise the putative functions of the fragments with TE insertions. Ninety-two primers amplifying 548 loci were used to detect variation in sequences associated with four different orders of TE sequences. TEs could be classed in ascending frequency into LTR-REs, TIRs, LINEs, SINEs and unknown TEs. The frequency of novel variation (putative activation) detected for the four orders of TEs was highest from the F1 to F2 generations, and lowest from the F2 to F3 generations. Functional annotation of sequences with TE insertions showed that genes with TE insertions were mainly involved in metabolic processes and binding, and preferentially functioned in organelles. TE variation in our study severely disturbed the genetic compositions of the different generations, resulting in inconsistencies in genetic clustering. Different types of TE showed different patterns of variation during the process of allopolyploidisation. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

Depth and substratum differentiations among coexisting herbivorous cichlids in Lake Tanganyika

PubMed Central

Ochi, Haruki

2016-01-01

Cichlid fish in Lake Tanganyika represent a system of adaptive radiation in which eight ancestral lineages have diversified into hundreds of species through adaptation to various niches. However, Tanganyikan cichlids have been thought to be oversaturated, that is, the species number exceeds the number of niches and ecologically equivalent and competitively even species coexist. However, recent studies have shed light on niche segregation on a finer scale among apparently equivalent species. We observed depth and substratum preferences of 15 herbivorous cichlids from four ecomorphs (i.e. grazer, browser, scraper and scooper) on a rocky littoral slope for 14 years. Depth differentiation was detected among grazers that defended feeding territories and among browsers with feeding territories. Cichlid species having no feeding territory also showed specificity on depth and substratum, resulting in habitat segregation among species that belong to the same ecomorph. Phylogenetically close species did not occupy adjacent depths, nor the opposite depth zones. Our findings suggest that apparently equivalent species of the same ecomorph coexist parapatrically along depth on a few-metre scale, or coexist with different substratum preferences on the rocky shore, and this niche segregation may have been acquired by competition between encountering equivalent species through repetitive lake-level fluctuations. PMID:28018609

Differential adaptation to a harsh granite outcrop habitat between sympatric Mimulus species.

PubMed

Ferris, Kathleen G; Willis, John H

2018-03-31

Understanding which environmental variables and traits underlie adaptation to harsh environments is difficult because many traits evolve simultaneously as populations or species diverge. Here, we investigate the ecological variables and traits that underlie Mimulus laciniatus' adaptation to granite outcrops compared to its sympatric, mesic-adapted progenitor, Mimulus guttatus. We use fine-scale measurements of soil moisture and herbivory to examine differences in selective forces between the species' habitats, and measure selection on flowering time, flower size, plant height, and leaf shape in a reciprocal transplant using M. laciniatus × M. guttatus F 4 hybrids. We find that differences in drought and herbivory drive survival differences between habitats, that M. laciniatus and M. guttatus are each better adapted to their native habitat, and differential habitat selection on flowering time, plant stature, and leaf shape. Although early flowering time, small stature, and lobed leaf shape underlie plant fitness in M. laciniatus' seasonally dry environment, increased plant size is advantageous in a competitive mesic environment replete with herbivores like M. guttatus'. Given that we observed divergent selection between habitats in the direction of species differences, we conclude that adaptation to different microhabitats is an important component of reproductive isolation in this sympatric species pair. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Progress in Understanding and Sequencing the Genome of Brassica rapa

PubMed Central

Hong, Chang Pyo; Kwon, Soo-Jin; Kim, Jung Sun; Yang, Tae-Jin; Park, Beom-Seok; Lim, Yong Pyo

2008-01-01

Brassica rapa, which is closely related to Arabidopsis thaliana, is an important crop and a model plant for studying genome evolution via polyploidization. We report the current understanding of the genome structure of B. rapa and efforts for the whole-genome sequencing of the species. The tribe Brassicaceae, which comprises ca. 240 species, descended from a common hexaploid ancestor with a basic genome similar to that of Arabidopsis. Chromosome rearrangements, including fusions and/or fissions, resulted in the present-day “diploid” Brassica species with variation in chromosome number and phenotype. Triplicated genomic segments of B. rapa are collinear to those of A. thaliana with InDels. The genome triplication has led to an approximately 1.7-fold increase in the B. rapa gene number compared to that of A. thaliana. Repetitive DNA of B. rapa has also been extensively amplified and has diverged from that of A. thaliana. For its whole-genome sequencing, the Brassica rapa Genome Sequencing Project (BrGSP) consortium has developed suitable genomic resources and constructed genetic and physical maps. Ten chromosomes of B. rapa are being allocated to BrGSP consortium participants, and each chromosome will be sequenced by a BAC-by-BAC approach. Genome sequencing of B. rapa will offer a new perspective for plant biology and evolution in the context of polyploidization. PMID:18288250

Honeydew feeding in the solitary bee Osmia bicornis as affected by aphid species and nectar availability.

PubMed

Konrad, Roger; Wäckers, Felix L; Romeis, Jörg; Babendreier, Dirk

2009-12-01

Like honey bees (Apis mellifera), non-Apis bees could exploit honeydew as a carbohydrate source. In addition to providing carbohydrates, this may expose them to potentially harmful plant products secreted in honeydew. However, knowledge on honeydew feeding by solitary bees is very scarce. Here we determine whether the polylectic solitary bee Osmia bicornis (=O. rufa) collects honeydew under semi-field conditions, and whether this is affected by aphid species and presence of floral nectar. Bees were provided with oilseed rape plants containing flowers and/or colonies of either Myzus persicae or Brevicoryne brassicae. We used the total sugar level of the bee crop as a measure of the individual's nutritional state and the oligosaccharide erlose as indicator for honeydew consumption. Erlose was present in honeydews from both aphid species, while absent in oilseed rape nectar, nor being synthesized by O. bicornis. When bees were confined to a single honeydew type as the only carbohydrate source, consumption of M. persicae honeydew was confirmed for 47% of the bees and consumption of B. brassicae honeydew for only 3%. Increased mortality in the latter treatment provided further evidence that B. brassicae honeydew is an unsuitable food source for O. bicornis. All bees that were given the choice between honeydew and floral nectar showed significantly increased total sugar levels. However, the fact that no erlose was detected in these bees indicates that honeydew was not consumed when suitable floral nectar was available. This study demonstrates that honeydew exploitation by O. bicornis is dependent on honeydew type and the presence of floral nectar.

Processing of Brassica seeds for feedstock in biofuels production

USDA-ARS?s Scientific Manuscript database

Several Brassica species are currently being evaluated to develop regionalized production systems based on their suitability to the environment and with the prevailing practices of growing commodity food crops like wheat, corn, and soybeans. This integrated approach to farming will provide high qual...

Phytotoxicity assay for seed production using Brassica rapa L.

EPA Science Inventory

Although pesticide drift can affect crop yield adversely, current plant testing protocols emphasize only the potential impacts on vegetative plant growth. The present study was conducted to determine whether a plant species with a short life cycle, such as Brassica rapa L. Wiscon...

Genome-Wide Survey and Characterization of Fatty Acid Desaturase Gene Family in Brassica napus and Its Parental Species.

PubMed

Xue, Yufei; Chen, Baojun; Wang, Rui; Win, Aung Naing; Li, Jiana; Chai, Yourong

2018-02-01

Rapeseed (Brassica napus) is an important oilseed crop worldwide, and fatty acid (FA) compositions determine the nutritional and economic value of its seed oil. Fatty acid desaturases (FADs) play a pivotal role in regulating FA compositions, but to date, no comprehensive genome-wide analysis of FAD gene family in rapeseed and its parent species has been reported. In this study, using homology searches, 84, 45, and 44 FAD genes were identified in rapeseed, Brassica rapa, and Brassica oleracea genomes, respectively. These FAD genes were unevenly located in 17 chromosomes and 2 scaffolds of rapeseed, 9 chromosomes and 1 scaffold of B. rapa, and all the chromosomes of B. oleracea. Phylogenetic analysis showed that the soluble and membrane-bound FADs in the three Brassica species were divided into four and six subfamilies, respectively. Generally, the soluble FADs contained two conserved histidine boxes, while three highly conserved histidine boxes were harbored in membrane-bound FADs. Exon-intron structure, intron phase, and motif composition and position were highly conserved in each FAD subfamily. Putative subcellular locations of FAD proteins in three Brassica species were consistent with those of corresponding known FADs. In total, 25 of simple sequence repeat (SSR) loci were found in FAD genes of the three Brassica species. Transcripts of selected FAD genes in the three species were examined in various organs/tissues or stress treatments from NCBI expressed sequence tag (EST) database. This study provides a critical molecular basis for quality improvement of rapeseed oil and facilitates our understanding of key roles of FAD genes in plant growth and development and stress response.

Erosion of Brassica incana Genetic Resources: Causes and Effects

NASA Astrophysics Data System (ADS)

Muscolo, A.; Settineri, G.; Mallamaci, C.; Papalia, T.; Sidari, M.

2017-07-01

Brassica incana Ten., possessing a number of useful agronomic traits, represents a precious genetic resource to be used in plant breeding programs to broaden the genetic base in most Brassica crop species. B. incana that grows on limestone cliffs is at risk of genetic erosion for environmental constraints and human activities. We studied the pedological conditions of a Calabrian site where the B. incana grows, and we correlated the soil properties to the physiological and biochemical aspects of B. incana to identify the causes and effects of the genetic erosion of this species. Our results evidenced that physical soil conditions did not affect B. incana growth and nutraceutical properties; conversely, biological soil properties modified its properties. We identified leaf pigments and secondary metabolites that can be used routinely as early warning indicators of plant threat, to evaluate in a short term the dynamic behavior of plants leading to species extinction.

Effect of Heavy Metals in Plants of the Genus Brassica

PubMed Central

Mourato, Miguel P.; Moreira, Inês N.; Leitão, Inês; Pinto, Filipa R.; Sales, Joana R.; Louro Martins, Luisa

2015-01-01

Several species from the Brassica genus are very important agricultural crops in different parts of the world and are also known to be heavy metal accumulators. There have been a large number of studies regarding the tolerance, uptake and defense mechanism in several of these species, notably Brassica juncea and B. napus, against the stress induced by heavy metals. Numerous studies have also been published about the capacity of these species to be used for phytoremediation purposes but with mixed results. This review will focus on the latest developments in the study of the uptake capacity, oxidative damage and biochemical and physiological tolerance and defense mechanisms to heavy metal toxicity on six economically important species: B. juncea, B. napus, B. oleracea, B. carinata, B. rapa and B. nigra. PMID:26247945

Recent progress in drought and salt tolerance studies in Brassica crops

PubMed Central

Zhang, Xuekun; Lu, Guangyuan; Long, Weihua; Zou, Xiling; Li, Feng; Nishio, Takeshi

2014-01-01

Water deficit imposed by either drought or salinity brings about severe growth retardation and yield loss of crops. Since Brassica crops are important contributors to total oilseed production, it is urgently needed to develop tolerant cultivars to ensure yields under such adverse conditions. There are various physiochemical mechanisms for dealing with drought and salinity in plants at different developmental stages. Accordingly, different indicators of tolerance to drought or salinity at the germination, seedling, flowering and mature stages have been developed and used for germplasm screening and selection in breeding practices. Classical genetic and modern genomic approaches coupled with precise phenotyping have boosted the unravelling of genes and metabolic pathways conferring drought or salt tolerance in crops. QTL mapping of drought and salt tolerance has provided several dozen target QTLs in Brassica and the closely related Arabidopsis. Many drought- or salt-tolerant genes have also been isolated, some of which have been confirmed to have great potential for genetic improvement of plant tolerance. It has been suggested that molecular breeding approaches, such as marker-assisted selection and gene transformation, that will enhance oil product security under a changing climate be integrated in the development of drought- and salt-tolerant Brassica crops. PMID:24987291

Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica.

PubMed

Yang, J; Liu, G; Zhao, N; Chen, S; Liu, D; Ma, W; Hu, Z; Zhang, M

2016-05-01

The genus Brassica has many species that are important for oil, vegetable and other food products. Three mitochondrial genome types (mitotype) originated from its common ancestor. In this paper, a B. nigra mitochondrial main circle genome with 232,407 bp was generated through de novo assembly. Synteny analysis showed that the mitochondrial genomes of B. rapa and B. oleracea had a better syntenic relationship than B. nigra. Principal components analysis and development of a phylogenetic tree indicated maternal ancestors of three allotetraploid species in Us triangle of Brassica. Diversified mitotypes were found in allotetraploid B. napus, in which napus-type B. napus was derived from B. oleracea, while polima-type B. napus was inherited from B. rapa. In addition, the mitochondrial genome of napus-type B. napus was closer to botrytis-type than capitata-type B. oleracea. The sub-stoichiometric shifting of several mitochondrial genes suggested that mitochondrial genome rearrangement underwent evolutionary selection during domestication and/or plant breeding. Our findings clarify the role of diploid species in the maternal origin of allotetraploid species in Brassica and suggest the possibility of breeding selection of the mitochondrial genome. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

Jasmonic acid-induced volatiles of Brassica oleracea attract parasitoids: effects of time and dose, and comparison with induction by herbivores

PubMed Central

Bruinsma, Maaike; Posthumus, Maarten A.; Mumm, Roland; Mueller, Martin J.; van Loon, Joop J. A.; Dicke, Marcel

2009-01-01

Caterpillar feeding induces direct and indirect defences in brassicaceous plants. This study focused on the role of the octadecanoid pathway in induced indirect defence in Brassica oleracea. The effect of induction by exogenous application of jasmonic acid (JA) on the responses of Brussels sprouts plants and on host-location behaviour of associated parasitoid wasps was studied. Feeding by the biting–chewing herbivores Pieris rapae and Plutella xylostella resulted in significantly increased endogenous levels of JA, a central component in the octadecanoid signalling pathway that mediates induced plant defence. The levels of the intermediate 12-oxophyto-dienoic acid (OPDA) were significantly induced only after P. rapae feeding. Three species of parasitoid wasps, Cotesia glomerata, C. rubecula, and Diadegma semiclausum, differing in host range and host specificity, were tested for their behavioural responses to volatiles from herbivore-induced, JA-induced, and non-induced plants. All three species were attracted to volatiles from JA-induced plants compared with control plants; however, they preferred volatiles from herbivore-induced plants over volatiles from JA-induced plants. Attraction of C. glomerata depended on both timing and dose of JA application. JA-induced plants produced larger quantities of volatiles than herbivore-induced and control plants, indicating that not only quantity, but also quality of the volatile blend is important in the host-location behaviour of the wasps. PMID:19451186

Evaluating the impact of sprouting conditions on the glucosinolate content of Brassica oleracea sprouts.

PubMed

Vale, A P; Santos, J; Brito, N V; Fernandes, D; Rosa, E; Oliveira, M Beatriz P P

2015-07-01

The glucosinolates content of brassica plants is a distinctive characteristic, representing a healthy advantage as many of these compounds are associated to antioxidant and anti-carcinogenic properties. Brassica sprouts are still an underutilized source of these bioactive compounds. In this work, four varieties of brassica sprouts (red cabbage, broccoli, Galega kale and Penca cabbage), including two local varieties from the North of Portugal, were grown to evaluate the glucosinolate profile and myrosinase activity during the sprouting. Also the influence of light/darkness exposure during sprouting on the glucosinolate content was assessed. Glucosinolate content and myrosinase activity of the sprouts was evaluated by HPLC methods. All sprouts revealed a higher content of aliphatic glucosinolates than of indole glucosinolates, contrary to the profile described for most of brassica mature plants. Galega kale sprouts had the highest glucosinolate content, mainly sinigrin and glucoiberin, which are recognized for their beneficial health effects. Penca cabbage sprouts were particularly richer in glucoraphanin, who was also one of the major compounds in broccoli sprouts. Red cabbage showed a higher content of progoitrin. Regarding myrosinase activity, Galega kale sprouts showed the highest values, revealing that the use of light/dark cycles and a sprouting phase of 7-9 days could be beneficial to preserve the glucosinolate content of this variety. Copyright © 2015 Elsevier Ltd. All rights reserved.

AFLP analysis of genetic diversity and phylogenetic relationships of Brassica oleracea in Ireland.

PubMed

El-Esawi, Mohamed A; Germaine, Kieran; Bourke, Paula; Malone, Renee

2016-01-01

Brassica oleracea L. is one of the most economically important vegetable crop species of the genus Brassica L. This species is threatened in Ireland, without any prior reported genetic studies. The use of this species is being very limited due to its imprecise phylogeny and uncompleted genetic characterisation. The main objective of this study was to assess the genetic diversity and phylogenetic relationships of a set of 25 Irish B. oleracea accessions using the powerful amplified fragment length polymorphism (AFLP) technique. A total of 471 fragments were scored across all the 11 AFLP primer sets used, out of which 423 (89.8%) were polymorphic and could differentiate the accessions analysed. The dendrogram showed that cauliflowers were more closely related to cabbages than kales were, and accessions of some cabbage types were distributed among different clusters within cabbage subgroups. Approximately 33.7% of the total genetic variation was found among accessions, and 66.3% of the variation resided within accessions. The total genetic diversity (HT) and the intra-accessional genetic diversity (HS) were 0.251 and 0.156, respectively. This high level of variation demonstrates that the Irish B. oleracea accessions studied should be managed and conserved for future utilisation and exploitation in food and agriculture. In conclusion, this study addressed important phylogenetic questions within this species, and provided a new insight into the inclusion of four accessions of cabbages and kales in future breeding programs for improving varieties. AFLP markers were efficient for assessing genetic diversity and phylogenetic relationships in Irish B. oleracea species. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

A novel Brassica-rhizotron system to unravel the dynamic changes in root system architecture of oilseed rape under phosphorus deficiency.

PubMed

Yuan, Pan; Ding, Guang-Da; Cai, Hong-Mei; Jin, Ke-Mo; Broadley, Martin Roger; Xu, Fang-Sen; Shi, Lei

2016-08-01

An important adaptation of plants to phosphorus (P) deficiency is to alter root system architecture (RSA) to increase P acquisition from the soil, but soil-based observations of RSA are technically challenging, especially in mature plants. The aim of this study was to investigate the root development and RSA of oilseed rape (Brassica napus L.) under low and high soil P conditions during an entire growth cycle. A new large Brassica-rhizotron system (approx. 118-litre volume) was developed to study the RSA dynamics of B. napus 'Zhongshuang11' in soils, using top-soils supplemented with low P (LP) or high P (HP) for a full plant growth period. Total root length (TRL), root tip number (RTN), root length density (RLD), biomass and seed yield traits were measured. TRL and RTN increased more rapidly in HP than LP plants from seedling to flowering stages. Both traits declined from flowering to silique stages, and then increased slightly in HP plants; in contrast, root senescence was observed in LP plants. RSA parameters measured from the polycarbonate plates were empirically consistent with analyses of excavated roots. Seed yield and shoot dry weights were closely associated positively with root dry weights, TRL, RLD and RTN at both HP and LP. The Brassica-rhizotron system is an effective method for soil-based root phenotyping across an entire growth cycle. Given that root senescence is likely to occur earlier under low P conditions, crop P deficiency is likely to affect late water and nitrogen uptake, which is critical for efficient resource use and optimal crop yields. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapa–B. oleracea monosomic alien addition lines

PubMed Central

Heneen, Waheeb K.; Geleta, Mulatu; Brismar, Kerstin; Xiong, Zhiyong; Pires, J. Chris; Hasterok, Robert; Stoute, Andrew I.; Scott, Roderick J.; King, Graham J.; Kurup, Smita

2012-01-01

Background and Aims Brassica rapa and B. oleracea are the progenitors of oilseed rape B. napus. The addition of each chromosome of B. oleracea to the chromosome complement of B. rapa results in a series of monosomic alien addition lines (MAALs). Analysis of MAALs determines which B. oleracea chromosomes carry genes controlling specific phenotypic traits, such as seed colour. Yellow-seeded oilseed rape is a desirable breeding goal both for food and livestock feed end-uses that relate to oil, protein and fibre contents. The aims of this study included developing a missing MAAL to complement an available series, for studies on seed colour control, chromosome homoeology and assignment of linkage groups to B. oleracea chromosomes. Methods A new batch of B. rapa–B. oleracea aneuploids was produced to generate the missing MAAL. Seed colour and other plant morphological features relevant to differentiation of MAALs were recorded. For chromosome characterization, Snow's carmine, fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used. Key Results The final MAAL was developed. Morphological traits that differentiated the MAALs comprised cotyledon number, leaf morphology, flower colour and seed colour. Seed colour was controlled by major genes on two B. oleracea chromosomes and minor genes on five other chromosomes of this species. Homoeologous pairing was largely between chromosomes with similar centromeric positions. FISH, GISH and a parallel microsatellite marker analysis defined the chromosomes in terms of their linkage groups. Conclusions A complete set of MAALs is now available for genetic, genomic, evolutionary and breeding perspectives. Defining chromosomes that carry specific genes, physical localization of DNA markers and access to established genetic linkage maps contribute to the integration of these approaches, manifested in the confirmed correspondence of linkage groups with specific chromosomes. Applications include marker

Sibling eating behaviours and differential child feeding practices reported by parents.

PubMed

Farrow, C V; Galloway, A T; Fraser, K

2009-04-01

The purpose of this study was to investigate the intra-familial relationships between parental reports of feeding practices used with siblings in the same family, and to evaluate whether differences in feeding practices are related to differences in siblings' eating behaviours. Eighty parents of two sibling children completed measures assessing their feeding practices and child eating behaviours. Parents reported using greater restrictive feeding practices with children who were fussier and desired to drink more than their sibling. Parents reported using more pressure to eat with siblings who were slower to eat, were fussier, emotionally under-ate, enjoyed food less, were less responsive to food, and were more responsive to internal satiety cues. Restriction and pressure to eat appear to be part of the non-shared environment which sibling children experience differently. These feeding practices may be used differently for children in the same family in response to child eating behaviours or other specific characteristics.

Comparison of bioactive phytochemical content and release of isothiocyanates in selected brassica sprouts.

PubMed

De Nicola, Gina Rosalinda; Bagatta, Manuela; Pagnotta, Eleonora; Angelino, Donato; Gennari, Lorenzo; Ninfali, Paolino; Rollin, Patrick; Iori, Renato

2013-11-01

The consumption of brassica sprouts as raw vegetables provides a fair amount of glucosinolates (GLs) and active plant myrosinase, which enables the breakdown of GLs into health-promoting isothiocyanates (ITCs). This study reports the determination of the main constituents related to human health found in edible sprouts of two Brassica oleracea varieties, broccoli and Tuscan black kale, and two Raphanus sativus varieties, Daikon and Sango. Radish sprouts exhibited the highest ability to produce ITCs, with Daikon showing the greatest level of conversion of GLs into bioactive ITCs (96.5%), followed by Sango (90.0%). Tuscan black kale gave a value of 68.5%, whereas broccoli displayed the lowest with 18.7%. ITCs were not the exclusive GL breakdown products in the two B. oleracea varieties, since nitriles were also produced, thus accounting for the lower conversion observed. Measuring the release of plant ITCs is a valuable tool in predicting the potential level of exposure to these bioactive compounds after the consumption of raw brassica sprouts. Copyright © 2013 Elsevier Ltd. All rights reserved.

Anthocyanins facilitate tungsten accumulation in Brassica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hale, K.L.

2002-11-01

Accumulation of molybdenum in Brassica was recently found to be correlated with anthocyanin content, involving the formation of a blue complex. Here the role of anthocyanins in tungsten sequestration was investigated using three species of Brassica: B. rapa (cv. Fast plants), B. juncea (Indian mustard) and B. oleracea (red cabbage). Seedlings of B. rapa and B. juncea turned blue when supplied with colourless tungstate. The blue compound co-localized with anthocyanins in the peripheral cell layers, and the degree of blueness was correlated with anthocyanin content. The direct involvement of anthocyanins in the blue coloration was evident when purified anthocyanins showedmore » a colour change from pink to blue in vitro upon addition of tungstate, over a wide pH range. Anthocyanin production was upregulated 3-fold by W in B. juncea, possibly reflecting a function for anthocyanins in W tolerance or sequestration. The presence of anthocyanins facilitated W accumulation in B. rapa: anthocyanin-containing seedlings accumulated 3-fold more W than an anthocyaninless mutant. There was no correlation between anthocyanin content and W tolerance under these conditions. The nature of the interaction between anthocyanins and tungstate was investigated. X-ray absorption spectroscopy showed no change in the local chemical environment of Wupon uptake of tungstate by the plant; HPLC analysis of purified anthocyanin with or without tungstate showed no peak shift after metal treatment.« less

Realizing the potential of rapid-cycling Brassica as a model system for use in plant biology research

NASA Technical Reports Server (NTRS)

Musgrave, M. E.

2000-01-01

Rapid-cycling Brassica populations were initially developed as a model for probing the genetic basis of plant disease. Paul Williams and co-workers selected accessions of the six main species for short time to flower and rapid seed maturation. Over multiple generations of breeding and selection, rapid-cycling populations of each of the six species were developed. Because of their close relationship with economically important Brassica species, rapid-cycling Brassica populations, especially those of B. rapa (RCBr) and B. oleracea, have seen wide application in plant and crop physiology investigations. Adding to the popularity of these small, short-lived plants for research applications is their extensive use in K-12 education and outreach.

Impact of foliar herbivory on the development of a root-feeding insect and its parasitoid

PubMed Central

Bezemer, T. Martijn; Cortesero, Anne Marie; Van der Putten, Wim H.; Vet, Louise E. M.; Harvey, Jeffrey A.

2007-01-01

The majority of studies exploring interactions between above- and below-ground biota have been focused on the effects of root-associated organisms on foliar herbivorous insects. This study examined the effects of foliar herbivory by Pieris brassicae L. (Lepidoptera: Pieridae) on the performance of the root herbivore Delia radicum L. (Diptera: Anthomyiidae) and its parasitoid Trybliographa rapae (Westwood) (Hymenoptera: Figitidae), mediated through a shared host plant Brassica nigra L. (Brassicaceae). In the presence of foliar herbivory, the survival of D. radicum and T. rapae decreased significantly by more than 50%. In addition, newly emerged adults of both root herbivores and parasitoids were significantly smaller on plants that had been exposed to foliar herbivory than on control plants. To determine what factor(s) may have accounted for the observed results, we examined the effects of foliar herbivory on root quantity and quality. No significant differences in root biomass were found between plants with and without shoot herbivore damage. Moreover, concentrations of nitrogen in root tissues were also unaffected by shoot damage by P. brassicae larvae. However, higher levels of indole glucosinolates were measured in roots of plants exposed to foliar herbivory, suggesting that the development of the root herbivore and its parasitoid may be, at least partly, negatively affected by increased levels of these allelochemicals in root tissues. Our results show that foliar herbivores can affect the development not only of root-feeding insects but also their natural enemies. We argue that such indirect interactions between above- and below-ground biota may play an important role in the structuring and functioning of communities. PMID:17334787

Enzymatic comparison and mortality of Beauveria bassiana against cabbage caterpillar Pieris brassicae LINN.

PubMed

Dhawan, Manish; Joshi, Neelam

Beauveria bassiana, an entomopathogenic fungus, is the alternative biocontrol agent exploited against major economic crop pests. Pieris brassicae L. is an emerging pest of the Brassicaceae family. Therefore, in the present study, fungal isolates of Beauveria bassiana, viz. MTCC 2028, MTCC 4495, MTCC 6291, and NBAII-11, were evaluated for their virulence against third instar larvae of P. brassicae. Among all these fungal isolates, maximum mortality (86.66%) was recorded in B. bassiana MTCC 4495 at higher concentration of spores (10 9 conidia/ml), and the minimum mortality (30.00%) was recorded in B. bassiana MTCC 6291 at a lower concentration (10 7 conidia/ml) after ten days of treatment. The extracellular cuticle-degrading enzyme activities of fungal isolates were measured. Variability was observed both in the pattern of enzyme secretion and the level of enzyme activities among various fungal isolates. B. bassiana MTCC 4495 recorded the maximum mean chitinase (0.51U/ml), protease (1.12U/ml), and lipase activities (1.36U/ml). The minimum mean chitinase and protease activities (0.37 and 0.91U/ml, respectively) were recorded in B. bassiana MTCC 6291. The minimum mean lipase activity (1.04U/ml) was recorded in B. bassiana NBAII-11. Our studies revealed B. bassiana MTCC 4495 as the most pathogenic isolate against P. brassicae, which also recorded maximum extracellular enzyme activities, suggesting the possible roles of extracellular enzymes in the pathogenicity of B. bassiana against P. brassicae. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Assembly and comparison of two closely related Brassica napus genomes.

PubMed

Bayer, Philipp E; Hurgobin, Bhavna; Golicz, Agnieszka A; Chan, Chon-Kit Kenneth; Yuan, Yuxuan; Lee, HueyTyng; Renton, Michael; Meng, Jinling; Li, Ruiyuan; Long, Yan; Zou, Jun; Bancroft, Ian; Chalhoub, Boulos; King, Graham J; Batley, Jacqueline; Edwards, David

2017-12-01

As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor-bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor-bzh contains a greater number of genes than the genome of Tapidor. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in future production of a B. napus pangenome. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Intraspecific Variation in Carotenoids of Brassica oleracea var. sabellica.

PubMed

Mageney, Vera; Baldermann, Susanne; Albach, Dirk C

2016-04-27

Carotenoids are best known as a source of natural antioxidants. Physiologically, carotenoids are part of the photoprotection in plants as they act as scavengers of reactive oxygen species (ROS). An important source of carotenoids in European food is Brassica oleracea. Focusing on the most abundant carotenoids, we estimated the contents of ß-carotene, (9Z)-neoxanthin, zeaxanthin, and lutein as well as those of chlorophylls a and b to assess their variability in Brassica oleracea var. sabellica. Our analyses included more than 30 cultivars categorized in five distinct sets grouped according to morphological characteristics or geographical origin. Our results demonstrated specific carotenoid patterns characteristic for American, Italian, and red-colored kale cultivars. Moreover, we demonstrated a tendency of high zeaxanthin proportions under traditional harvest conditions, which accord to low-temperature regimes. We also compared the carotenoid patterns of self-generated hybrid lines. Corresponding findings indicated that crossbreeding has a high potential for carotenoid content optimization in kale.

Consumption of a diet rich in Brassica vegetables is associated with a reduced abundance of sulphate‐reducing bacteria: A randomised crossover study

PubMed Central

Kellingray, Lee; Tapp, Henri S.; Saha, Shikha; Doleman, Joanne F.; Narbad, Arjan

2017-01-01

Scope We examined whether a Brassica‐rich diet was associated with an increase in the relative abundance of intestinal lactobacilli and sulphate‐reducing bacteria (SRB), or alteration to the composition of the gut microbiota, in healthy adults. Methods and results A randomised crossover study was performed with ten healthy adults who were fed a high‐ and a low‐Brassica diet for 2‐wk periods, with a 2‐wk washout phase separating the diets. The high‐Brassica diet consisted of six 84 g portions of broccoli, six 84 g portions of cauliflower and six 300 g portions of a broccoli and sweet potato soup. The low‐Brassica diet consisted of one 84 g portion of broccoli and one 84 g portion of cauliflower. Faecal microbiota composition was measured in samples collected following 2‐wk Brassica‐free periods (consumption of all Brassica prohibited), and after each diet, whereby the only Brassica consumed was that supplied by the study team. No significant changes to the relative abundance of lactobacilli were observed (p = 0.8019). The increased consumption of Brassica was associated with a reduction in the relative abundance of SRB (p = 0.0215), and members of the Rikenellaceae, Ruminococcaceae, Mogibacteriaceae, Clostridium and unclassified Clostridiales (p < 0.01). Conclusion The increased consumption of Brassica vegetables was linked to a reduced relative abundance of SRB, and therefore may be potentially beneficial to gastrointestinal health. PMID:28296348

Anatomy and transcript profiling of gynoecium development in female sterile Brassica napus mediated by one alien chromosome from Orychophragmus violaceus.

PubMed

Fu, Wen-qin; Zhao, Zhi-gang; Ge, Xian-hong; Ding, Li; Li, Zai-yun

2014-01-23

The gynoecium is one of the most complex organs of angiosperms specialized for seed production and dispersal, but only several genes important for ovule or embryo sac development were identified by using female sterile mutants. The female sterility in oilseed rape (Brassica napus) was before found to be related with one alien chromosome from another crucifer Orychophragmus violaceus. Herein, the developmental anatomy and comparative transcript profiling (RNA-seq) for the female sterility were performed to reveal the genes and possible metabolic pathways behind the formation of the damaged gynoecium. The ovules in the female sterile Brassica napus with two copies of the alien chromosomes (S1) initiated only one short integument primordium which underwent no further development and the female gametophyte development was blocked after the tetrad stage but before megagametogenesis initiation. Using Brassica_ 95k_ unigene as the reference genome, a total of 28,065 and 27,653 unigenes were identified to be transcribed in S1 and donor B. napus (H3), respectively. Further comparison of the transcript abundance between S1 and H3 revealed that 4540 unigenes showed more than two fold expression differences. Gene ontology and pathway enrichment analysis of the Differentially Expressed Genes (DEGs) showed that a number of important genes and metabolism pathways were involved in the development of gynoecium, embryo sac, ovule, integuments as well as the interactions between pollen and pistil. DEGs for the ovule development were detected to function in the metabolism pathways regulating brassinosteroid (BR) biosynthesis, adaxial/abaxial axis specification, auxin transport and signaling. A model was proposed to show the possible roles and interactions of these pathways for the sterile gynoecium development. The results provided new information for the molecular mechanisms behind the gynoecium development at early stage in B. napus.

Basis adaptation and domain decomposition for steady-state partial differential equations with random coefficients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

We present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support our construction with numericalmore » experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.« less

Feed efficiency of tropically adapted cattle when fed in winter or spring in a temperate location.

PubMed

Coleman, S W; Chase, C C; Phillips, W A; Riley, D G

2018-04-16

Earlier work has shown that young, tropically adapted cattle do not gain as rapidly as temperately adapted cattle during the winter in Oklahoma. The objective for this study was to determine if efficiency of gains was also impacted in tropically adapted cattle and if efficiency was consistent over different seasons. Over 3 yrs, 240 straightbred and crossbred steers (F1 and three-way crosses) of Angus, Brahman or Romosinuano breeding, born in Brooksville, FL were transported to El Reno, OK in October and fed in two phases to determine performance, individual intake and efficiency. Phase 1 (WIN) began in November after a 28 d recovery from shipping stress and Phase 2 (SS) began in March, 28 d following completion of WIN each year. The diet for WIN was a grower diet (14% CP, 1.10 Mcal NEg/kg) and that for the SS was a feedlot diet (12.8% CP; 1.33 Mcal NEg/kg). After a 14 d adjustment to diet and facilities, intake trials were conducted over a period of 56 to 162 d for determination of intake and gain for efficiency. Body weights were recorded at approximately 14 d intervals, and initial BW, median BW, and ADG were determined from individual animal regressions of BW on days on feed (DOF). Individual daily DMI was then regressed by phase on median BW and ADG, and residuals of regression were recorded as residual feed intake (RFI). Similarly, daily gain was regressed by phase on median BW and DMI, and errors of regression were recorded as residual gain (RADG). Gain to feed (G:F) was also calculated. The statistical model to evaluate ADG, DMI, and efficiency included fixed effects of dam age (3 to 4, 5, 6 to10, and > 10yr), harvest group (3 per year), age on test, and a nested term DT(ST x XB) where DT = proportion tropical breeding of dam (0, 0.5, or 1), ST= proportion tropical breeding of sire (1, or 0), and XB whether the calf was straightbred or crossbred. Year of record, sire(ST x XB) and pen were random effects. Pre-weaning ADG and BW increased (P < 0.05) with level

Development of Public Immortal Mapping Populations, Molecular Markers and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea

USDA-ARS?s Scientific Manuscript database

In this study we describe public immortal mapping populations of self-compatible lines, molecular markers, and linkage maps for Brassica rapa and B. oleracea. We propose that these resources are valuable reference tools for the Brassica community. The B. rapa population consists of 150 recombinant...

A model of the evolution of larval feeding rate in Drosophila driven by conflicting energy demands.

PubMed

Mueller, Laurence D; Barter, Thomas T

2015-02-01

Energy allocation is believed to drive trade-offs in life history evolution. We develop a physiological and genetic model of energy allocation that drives evolution of feeding rate in a well-studied model system. In a variety of stressful environments Drosophila larvae adapt by altering their rate of feeding. Drosophila larvae adapted to high levels of ammonia, urea, and the presence of parasitoids evolve lower feeding rates. Larvae adapted to crowded conditions evolve higher feeding rates. Feeding rates should affect gross food intake, metabolic rates, and efficiency of food utilization. We develop a model of larval net energy intake as a function of feeding rates. We show that when there are toxic compounds in the larval food that require energy for detoxification, larvae can maximize their energy intake by slowing their feeding rates. While the reduction in feeding rates may increase development time and decrease competitive ability, we show that genotypes with lower feeding rates can be favored by natural selection if they have a sufficiently elevated viability in the toxic environment. This work shows how a simple phenotype, larval feeding rates, may be of central importance in adaptation to a wide variety of stressful environments via its role in energy allocation.

NBR1 is a new PB1 signalling adapter in Th2 differentiation and allergic airway inflammation in vivo

PubMed Central

Yang, Jun-Qi; Liu, Hongzhu; Diaz-Meco, Maria T; Moscat, Jorge

2010-01-01

Allergic airway inflammation is a disease in which T helper 2 (Th2) cells have a critical function. The molecular mechanisms controlling Th2 differentiation and function are of paramount importance in biology and immunology. Recently, a network of PB1-containing adapters and kinases has been shown to be essential in this process owing to its function in regulating cell polarity and the activation of critical transcription factors. Here, we show in vivo data showing that T-cell-specific NBR1-deficient mice show impaired lung inflammation and have defective Th2 differentiation ex vivo with alterations in T-cell polarity and the selective inhibition of Gata3 and nuclear factor of activated T c1 activation. These results establish NBR1 as a novel PB1 adapter in Th2 differentiation and asthma. PMID:20808283

Circuit Motifs for Contrast-Adaptive Differentiation in Early Sensory Systems: The Role of Presynaptic Inhibition and Short-Term Plasticity

PubMed Central

Zhang, Danke; Wu, Si; Rasch, Malte J.

2015-01-01

In natural signals, such as the luminance value across of a visual scene, abrupt changes in intensity value are often more relevant to an organism than intensity values at other positions and times. Thus to reduce redundancy, sensory systems are specialized to detect the times and amplitudes of informative abrupt changes in the input stream rather than coding the intensity values at all times. In theory, a system that responds transiently to fast changes is called a differentiator. In principle, several different neural circuit mechanisms exist that are capable of responding transiently to abrupt input changes. However, it is unclear which circuit would be best suited for early sensory systems, where the dynamic range of the natural input signals can be very wide. We here compare the properties of different simple neural circuit motifs for implementing signal differentiation. We found that a circuit motif based on presynaptic inhibition (PI) is unique in a sense that the vesicle resources in the presynaptic site can be stably maintained over a wide range of stimulus intensities, making PI a biophysically plausible mechanism to implement a differentiator with a very wide dynamical range. Moreover, by additionally considering short-term plasticity (STP), differentiation becomes contrast adaptive in the PI-circuit but not in other potential neural circuit motifs. Numerical simulations show that the behavior of the adaptive PI-circuit is consistent with experimental observations suggesting that adaptive presynaptic inhibition might be a good candidate neural mechanism to achieve differentiation in early sensory systems. PMID:25723493

Circuit motifs for contrast-adaptive differentiation in early sensory systems: the role of presynaptic inhibition and short-term plasticity.

PubMed

Zhang, Danke; Wu, Si; Rasch, Malte J

2015-01-01

In natural signals, such as the luminance value across of a visual scene, abrupt changes in intensity value are often more relevant to an organism than intensity values at other positions and times. Thus to reduce redundancy, sensory systems are specialized to detect the times and amplitudes of informative abrupt changes in the input stream rather than coding the intensity values at all times. In theory, a system that responds transiently to fast changes is called a differentiator. In principle, several different neural circuit mechanisms exist that are capable of responding transiently to abrupt input changes. However, it is unclear which circuit would be best suited for early sensory systems, where the dynamic range of the natural input signals can be very wide. We here compare the properties of different simple neural circuit motifs for implementing signal differentiation. We found that a circuit motif based on presynaptic inhibition (PI) is unique in a sense that the vesicle resources in the presynaptic site can be stably maintained over a wide range of stimulus intensities, making PI a biophysically plausible mechanism to implement a differentiator with a very wide dynamical range. Moreover, by additionally considering short-term plasticity (STP), differentiation becomes contrast adaptive in the PI-circuit but not in other potential neural circuit motifs. Numerical simulations show that the behavior of the adaptive PI-circuit is consistent with experimental observations suggesting that adaptive presynaptic inhibition might be a good candidate neural mechanism to achieve differentiation in early sensory systems.

Differentiated adaptive evolution, episodic relaxation of selective constraints, and pseudogenization of umami and sweet taste genes TAS1Rs in catarrhine primates.

PubMed

Liu, Guangjian; Walter, Lutz; Tang, Suni; Tan, Xinxin; Shi, Fanglei; Pan, Huijuan; Roos, Christian; Liu, Zhijin; Li, Ming

2014-01-01

Umami and sweet tastes are two important basic taste perceptions that allow animals to recognize diets with nutritious carbohydrates and proteins, respectively. Until recently, analyses of umami and sweet taste were performed on various domestic and wild animals. While most of these studies focused on the pseudogenization of taste genes, which occur mostly in carnivores and species with absolute feeding specialization, omnivores and herbivores were more or less neglected. Catarrhine primates are a group of herbivorous animals (feeding mostly on plants) with significant divergence in dietary preference, especially the specialized folivorous Colobinae. Here, we conducted the most comprehensive investigation to date of selection pressure on sweet and umami taste genes (TAS1Rs) in catarrhine primates to test whether specific adaptive evolution occurred during their diversification, in association with particular plant diets. We documented significant relaxation of selective constraints on sweet taste gene TAS1R2 in the ancestral branch of Colobinae, which might correlate with their unique ingestion and digestion of leaves. Additionally, we identified positive selection acting on Cercopithecidae lineages for the umami taste gene TAS1R1, on the Cercopithecinae and extant Colobinae and Hylobatidae lineages for TAS1R2, and on Macaca lineages for TAS1R3. Our research further identified several site mutations in Cercopithecidae, Colobinae and Pygathrix, which were detected by previous studies altering the sensitivity of receptors. The positively selected sites were located mostly on the extra-cellular region of TAS1Rs. Among these positively selected sites, two vital sites for TAS1R1 and four vital sites for TAS1R2 in extra-cellular region were identified as being responsible for the binding of certain sweet and umami taste molecules through molecular modelling and docking. Our results suggest that episodic and differentiated adaptive evolution of TAS1Rs pervasively occurred

The Infant Feeding Genogram: a tool for exploring family infant feeding history and identifying support needs.

PubMed

Darwent, K L; McInnes, R J; Swanson, V

2016-10-19

Family culture and beliefs are passed through the generations within families and influence what constitutes appropriate infant care. This includes infant feeding decisions where a family history and support network congruent with women's infant feeding intentions has been shown to be important to women's breastfeeding experience. This is reflected in breastfeeding rates where women who were not breastfed themselves are less likely to initiate and continue with breastfeeding. Given the importance of family infant feeding history in the initiation and duration of breastfeeding, and the limited ability of some families to provide support; it is unclear why infant feeding family history and support networks are not explored during pregnancy. The Infant Feeding Genogram was adapted from a simple pictorial device that is widely used in psychotherapy and genetic counselling. This tool was developed as part of a study investigating the experience of women when they were the first to breastfeed in their family. Fourteen Scottish participants completed their Infant Feeding Genogram as part of a semi-structured interview. The tool was adapted alongside their narratives to give a visual representation of each participant's family infant feeding history. The utility of the genogram is illustrated through two contrasting case examples with very different family feeding histories. The genogram showed family structures, patterns of infant feeding over time, and supportive or conflicting relationships. In the research setting it assisted women to explore their infant feeding history, identify challenges and sources of support and build rapport with the interviewer. The infant feeding genogram is proposed as a time efficient tool that could assist health professionals and other breastfeeding workers to support women and their families and by stimulating discussion around breastfeeding, Bby identifying strengths or possible deficits in social support for each individual, the tool

Differential transfer processes in incremental visuomotor adaptation.

PubMed

Seidler, Rachel D

2005-01-01

Visuomotor adaptive processes were examined by testing transfer of adaptation between similar conditions. Participants made manual aiming movements with a joystick to hit targets on a computer screen, with real-time feedback display of their movement. They adapted to three different rotations of the display in a sequential fashion, with a return to baseline display conditions between rotations. Adaptation was better when participants had prior adaptive experiences. When performance was assessed using direction error (calculated at the time of peak velocity) and initial endpoint error (error before any overt corrective actions), transfer was greater when the final rotation reflected an addition of previously experienced rotations (adaptation order 30 degrees rotation, 15 degrees, 45 degrees) than when it was a subtraction of previously experienced conditions (adaptation order 45 degrees rotation, 15 degrees, 30 degrees). Transfer was equal regardless of adaptation order when performance was assessed with final endpoint error (error following any discrete, corrective actions). These results imply the existence of multiple independent processes in visuomotor adaptation.

A new Secondary metabolites of the crinoid (Comanthina schlegeli) associated fungus Alternaria brassicae 93.

PubMed

Zhang, Liu-Hong; Wang, Hong-Wei; Xu, Jia-Yi; Li, Jing; Liu, Lan

2016-10-01

Fungus Alternaria brassicae 93 isolated from crinoid (Comanthina schlegeli), which was collected from the South China Sea. Six compounds were isolated from A. brassicae 93, including one new compound (1), along with five known compounds, ochratoxin A methyl ester (2), cis-4-hydroxym-ellein (3), (R)-7-hydroxymellein (4), trans-2-anhydromevalonic (5) and protocatechuic acid (6). Their structures were determined by spectroscopic methods and comparison with reported data. Cytotoxicity against two human cancer cell lines and antibacterial activity against twelve aquatic bacteria of compound 1 were also tested.

Feed gas contaminant control in ion transport membrane systems

DOEpatents

Carolan, Michael Francis [Allentown, PA; Minford, Eric [Laurys Station, PA; Waldron, William Emil [Whitehall, PA

2009-07-07

Ion transport membrane oxidation system comprising an enclosure having an interior and an interior surface, inlet piping having an internal surface and adapted to introduce a heated feed gas into the interior of the enclosure, and outlet piping adapted to withdraw a product gas from the interior of the enclosure; one or more planar ion transport membrane modules disposed in the interior of the enclosure, each membrane module comprising mixed metal oxide material; and a preheater adapted to heat a feed gas to provide the heated feed gas to the inlet piping, wherein the preheater comprises an interior surface. Any of the interior surfaces of the enclosure, the inlet piping, and the preheater may be lined with a copper-containing metal lining. Alternatively, any of the interior surfaces of the inlet piping and the preheater may be lined with a copper-containing metal lining and the enclosure may comprise copper.

A novel composite adaptive flap controller design by a high-efficient modified differential evolution identification approach.

PubMed

Li, Nailu; Mu, Anle; Yang, Xiyun; Magar, Kaman T; Liu, Chao

2018-05-01

The optimal tuning of adaptive flap controller can improve adaptive flap control performance on uncertain operating environments, but the optimization process is usually time-consuming and it is difficult to design proper optimal tuning strategy for the flap control system (FCS). To solve this problem, a novel adaptive flap controller is designed based on a high-efficient differential evolution (DE) identification technique and composite adaptive internal model control (CAIMC) strategy. The optimal tuning can be easily obtained by DE identified inverse of the FCS via CAIMC structure. To achieve fast tuning, a high-efficient modified adaptive DE algorithm is proposed with new mutant operator and varying range adaptive mechanism for the FCS identification. A tradeoff between optimized adaptive flap control and low computation cost is successfully achieved by proposed controller. Simulation results show the robustness of proposed method and its superiority to conventional adaptive IMC (AIMC) flap controller and the CAIMC flap controllers using other DE algorithms on various uncertain operating conditions. The high computation efficiency of proposed controller is also verified based on the computation time on those operating cases. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Effects of supplementary lighting by natural light for growth of Brassica chinensis

NASA Astrophysics Data System (ADS)

Yeh, Shih-Chuan; Lee, Hui-Ping; Kao, Shih-Tse; Lu, Ju-Lin

2016-04-01

This paper present a model of cultivated chamber with supplementary natural colour light. We investigate the effects of supplementary natural red light and natural blue light on growth of Brassica chinensis under natural white light illumination. After 4 weeks of supplementary colour light treatment, the experiment results shown that the weight of fresh leaf were not affected by supplementary natural blue light. However, those Brassica chinensis were cultivated in the chambers with supplementary natural red light obtained a significant increasing of fresh weight of leaf under both white light illuminate models. The combination of natural white light with supplementary natural red light illumination will be benefits in growth for cultivation and energy saving.

Adaptive Epigenetic Differentiation between Upland and Lowland Rice Ecotypes Revealed by Methylation-Sensitive Amplified Polymorphism.

PubMed

Xia, Hui; Huang, Weixia; Xiong, Jie; Tao, Tao; Zheng, Xiaoguo; Wei, Haibin; Yue, Yunxia; Chen, Liang; Luo, Lijun

2016-01-01

The stress-induced epimutations could be inherited over generations and play important roles in plant adaption to stressful environments. Upland rice has been domesticated in water-limited environments for thousands of years and accumulated drought-induced epimutations of DNA methylation, making it epigenetically differentiated from lowland rice. To study the epigenetic differentiation between upland and lowland rice ecotypes on their drought-resistances, the epigenetic variation was investigated in 180 rice landraces under both normal and osmotic conditions via methylation-sensitive amplified polymorphism (MSAP) technique. Great alterations (52.9~54.3% of total individual-locus combinations) of DNA methylation are recorded when rice encountering the osmotic stress. Although the general level of epigenetic differentiation was very low, considerable level of ΦST (0.134~0.187) was detected on the highly divergent epiloci (HDE). The HDE detected in normal condition tended to stay at low levels in upland rice, particularly the ones de-methylated in responses to osmotic stress. Three out of four selected HDE genes differentially expressed between upland and lowland rice under normal or stressed conditions. Moreover, once a gene at HDE was up-/down-regulated in responses to the osmotic stress, its expression under the normal condition was higher/lower in upland rice. This result suggested expressions of genes at the HDE in upland rice might be more adaptive to the osmotic stress. The epigenetic divergence and its influence on the gene expression should contribute to the higher drought-resistance in upland rice as it is domesticated in the water-limited environment.

Adaptive Epigenetic Differentiation between Upland and Lowland Rice Ecotypes Revealed by Methylation-Sensitive Amplified Polymorphism

PubMed Central

Xiong, Jie; Tao, Tao; Zheng, Xiaoguo; Wei, Haibin; Yue, Yunxia; Chen, Liang; Luo, Lijun

2016-01-01

The stress-induced epimutations could be inherited over generations and play important roles in plant adaption to stressful environments. Upland rice has been domesticated in water-limited environments for thousands of years and accumulated drought-induced epimutations of DNA methylation, making it epigenetically differentiated from lowland rice. To study the epigenetic differentiation between upland and lowland rice ecotypes on their drought-resistances, the epigenetic variation was investigated in 180 rice landraces under both normal and osmotic conditions via methylation-sensitive amplified polymorphism (MSAP) technique. Great alterations (52.9~54.3% of total individual-locus combinations) of DNA methylation are recorded when rice encountering the osmotic stress. Although the general level of epigenetic differentiation was very low, considerable level of ΦST (0.134~0.187) was detected on the highly divergent epiloci (HDE). The HDE detected in normal condition tended to stay at low levels in upland rice, particularly the ones de-methylated in responses to osmotic stress. Three out of four selected HDE genes differentially expressed between upland and lowland rice under normal or stressed conditions. Moreover, once a gene at HDE was up-/down-regulated in responses to the osmotic stress, its expression under the normal condition was higher/lower in upland rice. This result suggested expressions of genes at the HDE in upland rice might be more adaptive to the osmotic stress. The epigenetic divergence and its influence on the gene expression should contribute to the higher drought-resistance in upland rice as it is domesticated in the water-limited environment. PMID:27380174

Cold-Induced Accumulation of hsp90 Transcripts in Brassica napus.

PubMed Central

Krishna, P.; Sacco, M.; Cherutti, J. F.; Hill, S.

1995-01-01

Characterization of the expression of hsp90 genes of Brassica napus by northern blot analysis and immunoblotting showed that the hsp90 mRNA and protein are present in all B. napus tissues examined, albeit at different levels. High levels of hsp90 mRNA and protein were found in young and rapidly dividing tissues such as shoot apices and flower buds, suggesting that hsp90 may have an important role in plant growth and development. A significant increase in hsp90 mRNA levels was detected in seedlings exposed to 5[deg]C. The transcript levels reached a maximum within 1 d of cold treatment and remained elevated for the entire duration of cold treatment. The levels of hsp90 mRNA rapidly decreased to the level found in control plants upon return to 20[deg]C. The cold-induced accumulation of hsp90 mRNA closely resembles the expression of two previously identified cold-regulated genes of B. napus. We have also confirmed cold regulation of hsp90 mRNA in spinach (Spinacea oleracea). Our results suggest a role for hsp90 in adaptation to cold temperature stress. PMID:12228411

Feeding and Reward Are Differentially Induced by Activating GABAergic Lateral Hypothalamic Projections to VTA.

PubMed

Barbano, M Flavia; Wang, Hui-Ling; Morales, Marisela; Wise, Roy A

2016-03-09

Electrical stimulation of the lateral hypothalamus (LH) has two motivational effects: long trains of stimulation induce drive-like effects such as eating, and short trains are rewarding. It has not been clear whether a single set of activated fibers subserves the two effects. Previous optogenetic stimulation studies have confirmed that reinforcement and induction of feeding can each be induced by selective stimulation of GABAergic fibers originating in the bed nucleus of the LH and projecting to the ventral tegmental area (VTA). In the present study we determined the optimal stimulation parameters for each of the two optogenetically induced effects in food-sated mice. Stimulation-induced eating was strongest with 5 Hz and progressively weaker with 10 and 20 Hz. Stimulation-induced reward was strongest with 40 Hz and progressively weaker with lower or higher frequencies. Mean preferred duration for continuous 40 Hz stimulation was 61.6 s in a "real-time" place preference task; mean preferred duration for 5 Hz stimulation was 45.6 s. The differential effects of high- and low-frequency stimulation of this pathway seem most likely to be due to differential effects on downstream targets. Copyright © 2016 the authors 0270-6474/16/362975-11$15.00/0.

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis

PubMed Central

Mason, Annaliese S.; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E.; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A. P.; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N.

2016-01-01

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. PMID:26614742

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.

PubMed

Mason, Annaliese S; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A P; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N

2016-02-01

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. Copyright © 2016 by the Genetics Society of America.

Complementary effect of natural and sexual selection against immigrants maintains differentiation between locally adapted fish

NASA Astrophysics Data System (ADS)

Plath, Martin; Riesch, Rüdiger; Oranth, Alexandra; Dzienko, Justina; Karau, Nora; Schießl, Angela; Stadler, Stefan; Wigh, Adriana; Zimmer, Claudia; Arias-Rodriguez, Lenin; Schlupp, Ingo; Tobler, Michael

2010-08-01

Adaptation to ecologically heterogeneous environments can drive speciation. But what mechanisms maintain reproductive isolation among locally adapted populations? Using poeciliid fishes in a system with naturally occurring toxic hydrogen sulfide, we show that (a) fish from non-sulfidic sites ( Poecilia mexicana) show high mortality (95 %) after 24 h when exposed to the toxicant, while locally adapted fish from sulfidic sites ( Poecilia sulphuraria) experience low mortality (13 %) when transferred to non-sulfidic water. (b) Mate choice tests revealed that P. mexicana females exhibit a preference for conspecific males in non-sulfidic water, but not in sulfidic water, whereas P. sulphuraria females never showed a preference. Increased costs of mate choice in sulfidic, hypoxic water, and the lack of selection for reinforcement due to the low survival of P. mexicana may explain the absence of a preference in P. sulphuraria females. Taken together, our study may be the first to demonstrate independent—but complementary—effects of natural and sexual selection against immigrants maintaining differentiation between locally adapted fish populations.

Complementary effect of natural and sexual selection against immigrants maintains differentiation between locally adapted fish.

PubMed

Plath, Martin; Riesch, Rüdiger; Oranth, Alexandra; Dzienko, Justina; Karau, Nora; Schiessl, Angela; Stadler, Stefan; Wigh, Adriana; Zimmer, Claudia; Arias-Rodriguez, Lenin; Schlupp, Ingo; Tobler, Michael

2010-08-01

Adaptation to ecologically heterogeneous environments can drive speciation. But what mechanisms maintain reproductive isolation among locally adapted populations? Using poeciliid fishes in a system with naturally occurring toxic hydrogen sulfide, we show that (a) fish from non-sulfidic sites (Poecilia mexicana) show high mortality (95 %) after 24 h when exposed to the toxicant, while locally adapted fish from sulfidic sites (Poecilia sulphuraria) experience low mortality (13 %) when transferred to non-sulfidic water. (b) Mate choice tests revealed that P. mexicana females exhibit a preference for conspecific males in non-sulfidic water, but not in sulfidic water, whereas P. sulphuraria females never showed a preference. Increased costs of mate choice in sulfidic, hypoxic water, and the lack of selection for reinforcement due to the low survival of P. mexicana may explain the absence of a preference in P. sulphuraria females. Taken together, our study may be the first to demonstrate independent-but complementary-effects of natural and sexual selection against immigrants maintaining differentiation between locally adapted fish populations.

Genome-wide identification and role of MKK and MPK gene families in clubroot resistance of Brassica rapa.

PubMed

Piao, Yinglan; Jin, Kaining; He, Ying; Liu, Jiaxiu; Liu, Shuang; Li, Xiaonan; Piao, Zhongyun

2018-01-01

Mitogen-activated protein kinase (MAPK or MPK) cascades play key roles in responses to various biotic stresses, as well as in plant growth and development. However, the responses of MPK and MPK kinase (MKK) in Chinese cabbage (Brassica rapa ssp. pekinensis) to Plasmodiophora brassicae, a causal agent of clubroot disease in Brassica crops, are still not clear. In the present study, a total of 11 B. rapa MKK (BraMKK) and 30 BraMPK genes were identified and unevenly distributed in 6 and 10 chromosomes, respectively. The synteny analysis indicated that these genes experienced whole-genome triplication and segmental and tandem duplication during or after the divergence of B. rapa, accompanied by the loss of three MKK and two MPK orthologs of Arabidopsis. The BraMKK and BraMPK genes were classified into four groups with similar intron/exon structures and conserved motifs in each group. A quantitative PCR analysis showed that the majority of BraMKK and BraMPK genes were natively expressed in roots, hypocotyls, and leaves, whereas 5 BraMKK and 16 BraMPK genes up-regulated in the roots upon P. brassicae infection. Additionally, these 5 BraMKK and 16 BraMPK genes exhibited a significantly different expression pattern between a pair of clubroot-resistant/susceptible near-isogenic lines (NILs). Furthermore, the possible modules of MKK-MPK involved in B. rapa-P. brassicae interaction are also discussed. The present study will provide functional clues for further characterization of the MAPK cascades in B. rapa.

Plant Chemistry and Local Adaptation of a Specialized Folivore

PubMed Central

Laukkanen, Liisa; Leimu, Roosa; Muola, Anne; Lilley, Marianna; Salminen, Juha-Pekka; Mutikainen, Pia

2012-01-01

Local adaptation is central for creating and maintaining spatial variation in plant-herbivore interactions. Short-lived insect herbivores feeding on long-lived plants are likely to adapt to their local host plants, because of their short generation time, poor dispersal, and geographically varying selection due to variation in plant defences. In a reciprocal feeding trial, we investigated the impact of geographic variation in plant secondary chemistry of a long-lived plant, Vincetoxicum hirundinaria, on among-population variation in local adaptation of a specialist leaf-feeding herbivore, Abrostola asclepiadis. The occurrence and degree of local adaptation varied among populations. This variation correlated with qualitative and quantitative differences in plant chemistry among the plant populations. These findings provide insights into the mechanisms driving variation in local adaptation in this specialized plant-herbivore interaction. PMID:22666493

Neofunctionalization of Duplicated Tic40 Genes Caused a Gain-of-Function Variation Related to Male Fertility in Brassica oleracea Lineages1[W][OPEN

PubMed Central

Dun, Xiaoling; Shen, Wenhao; Hu, Kaining; Zhou, Zhengfu; Xia, Shengqian; Wen, Jing; Yi, Bin; Shen, Jinxiong; Ma, Chaozhi; Tu, Jinxing; Fu, Tingdong; Lagercrantz, Ulf

2014-01-01

Gene duplication followed by functional divergence in the event of polyploidization is a major contributor to evolutionary novelties. The Brassica genus evolved from a common ancestor after whole-genome triplication. Here, we studied the evolutionary and functional features of Brassica spp. homologs to Tic40 (for translocon at the inner membrane of chloroplasts with 40 kDa). Four Tic40 loci were identified in allotetraploid Brassica napus and two loci in each of three basic diploid Brassica spp. Although these Tic40 homologs share high sequence identities and similar expression patterns, they exhibit altered functional features. Complementation assays conducted on Arabidopsis thaliana tic40 and the B. napus male-sterile line 7365A suggested that all Brassica spp. Tic40 homologs retain an ancestral function similar to that of AtTic40, whereas BolC9.Tic40 in Brassica oleracea and its ortholog in B. napus, BnaC9.Tic40, in addition, evolved a novel function that can rescue the fertility of 7365A. A homologous chromosomal rearrangement placed bnac9.tic40 originating from the A genome (BraA10.Tic40) as an allele of BnaC9.Tic40 in the C genome, resulting in phenotypic variation for male sterility in the B. napus near-isogenic two-type line 7365AB. Assessment of the complementation activity of chimeric B. napus Tic40 domain-swapping constructs in 7365A suggested that amino acid replacements in the carboxyl terminus of BnaC9.Tic40 cause this functional divergence. The distribution of these amino acid replacements in 59 diverse Brassica spp. accessions demonstrated that the neofunctionalization of Tic40 is restricted to B. oleracea and its derivatives and thus occurred after the divergence of the Brassica spp. A, B, and C genomes. PMID:25185122

Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species.

PubMed

Ronkin, Dana; Seroussi, Eyal; Nitzan, Tali; Doron-Faigenboim, Adi; Cnaani, Avner

2015-03-01

Tilapias are a group of freshwater species, which vary in their ability to adapt to high salinity water. Osmotic regulation in fish is conducted mainly in the gills, kidney, and gastrointestinal tract (GIT). The mechanisms involved in ion and water transport through the GIT is not well-characterized, with only a few described complexes. Comparing the transcriptome of the anterior and posterior intestinal sections of a freshwater and saltwater adapted fish by deep-sequencing, we examined the salinity adaptation of two tilapia species: the high salinity-tolerant Oreochromis mossambicus (Mozambique tilapia), and the less salinity-tolerant Oreochromis niloticus (Nile tilapia). This comparative analysis revealed high similarity in gene expression response to salinity change between species in the posterior intestine and large differences in the anterior intestine. Furthermore, in the anterior intestine 68 genes were saltwater up-regulated in one species and down-regulated in the other species (47 genes up-regulated in O. niloticus and down-regulated in O. mossambicus, with 21 genes showing the reverse pattern). Gene ontology (GO) analysis showed a high proportion of transporter and ion channel function among these genes. The results of this study point to a group of genes that differed in their salinity-dependent regulation pattern in the anterior intestine as potentially having a role in the differential salinity tolerance of these two closely related species. Copyright © 2015 Elsevier Inc. All rights reserved.

Parasite-altered feeding behavior in insects: integrating functional and mechanistic research frontiers.

PubMed

Bernardo, Melissa A; Singer, Michael S

2017-08-15

Research on parasite-altered feeding behavior in insects is contributing to an emerging literature that considers possible adaptive consequences of altered feeding behavior for the host or the parasite. Several recent ecoimmunological studies show that insects can adaptively alter their foraging behavior in response to parasitism. Another body of recent work shows that infection by parasites can change the behavior of insect hosts to benefit the parasite; manipulations of host feeding behavior may be part of this phenomenon. Here, we address both the functional and the underlying physiological frontiers of parasite-altered feeding behavior in order to spur research that better integrates the two. Functional categories of parasite-altered behavior that are adaptive for the host include prophylaxis, therapy and compensation, while host manipulation is adaptive for the parasite. To better understand and distinguish prophylaxis, therapy and compensation, further study of physiological feedbacks affecting host sensory systems is especially needed. For host manipulation in particular, research on mechanisms by which parasites control host feedbacks will be important to integrate with functional approaches. We see this integration as critical to advancing the field of parasite-altered feeding behavior, which may be common in insects and consequential for human and environmental health. © 2017. Published by The Company of Biologists Ltd.

Influence of microgravity on ultrastructure and storage reserves in seeds of Brassica rapa L

NASA Technical Reports Server (NTRS)

Kuang, A.; Xiao, Y.; McClure, G.; Musgrave, M. E.

2000-01-01

Successful plant reproduction under spaceflight conditions has been problematic in the past. During a 122 d opportunity on the Mir space station, full life cycles of Brassica rapa L. were completed in microgravity in a series of three experiments in the Svet greenhouse. Ultrastructural and cytochemical analyses of storage reserves in mature dry seeds produced in these experiments were compared with those of seeds produced during a high-fidelity ground control. Additional analyses were performed on developing Brassica embryos, 15 d post pollination, which were produced during a separate experiment on the Shuttle (STS-87). Seeds produced on Mir had less than 20% of the cotyledon cell number found in seeds harvested from the ground control. Cytochemical localization of storage reserves in mature cotyledons showed that starch was retained in the spaceflight material, whereas protein and lipid were the primary storage reserves in ground control seeds. Protein bodies in mature cotyledons produced in space were 44% smaller than those in the ground control seeds. Fifteen days after pollination, cotyledon cells from mature embryos formed in space had large numbers of starch grains, and protein bodies were absent, while in developing ground control seeds at the same stage, protein bodies had already formed and fewer starch grains were evident. These data suggest that both the late stage of seed development and maturation are changed in Brassica by growth in a microgravity environment. While gravity is not absolutely required for any step in the plant life cycle, seed quality in Brassica is compromised by development in microgravity.

Transformation of Arabidopsis with a Brassica SLG/SRK region and ARC1 gene is not sufficient to transfer the self-incompatibility phenotype.

PubMed

Bi, Y M; Brugière, N; Cui, Y; Goring, D R; Rothstein, S J

2000-05-01

Self-incompatibility (SI) promotes outbreeding in flowering plants, and in Brassica SI is genetically controlled by the S locus. Self-incompatible Brassica and self-fertile Arabidopsis belong to the same crucifer family. In addition, a comparative analysis reveals a high degree of microsynteny between the B. campestris S locus and its homologous region in Arabidopsis--with the notable exception that the Brassica SI genes, SLG and SRK, are missing. Brassica ARC1 encodes a component of the SRK signal transduction pathway leading to self-pollen rejection, and no closely related ARC1 homolog has been identified in Arabidopsis. The purpose of the research reported here was to introduce Brassica SI components into Arabidopsis in an attempt to compensate for the missing genes and to investigate whether the SI phenotype can be transferred. Inserts of approximately 40 kb from the fosmid clones F20 and F22, which span the B. napus W1 SLG-SRK region, were cloned into the plant transformation vector pBIBAC2. Transgenic plants were generated that expressed the Brassica SI genes in the flower buds. In addition, the endogenous, SLG-like, gene AtS1 was not co-suppressed by the Brassica SLG transgene. No SI phenotype was observed among the T1 BIBAC2-F20 and BIBAC2-F22 transgenic plants. When the ARC1 gene was transformed into BIBAC2-F20 or BIBAC2-F22 plants, the resulting BIBAC2-F20-ARC1 and BIBAC2-F22-ARC1 plants still set seeds normally, and no rejection response was observed when self-incompatible B. napus W1 pollen was placed on BIBAC2-F20-ARC1 or BIBAC2-F22-ARC1 Arabidopsis stigmas. Taken together, our results suggest that complementing Arabidopsis genome with Brassica SLG, SRK and ARC1 genes is unlikely to be sufficient to transfer the SI phenotype.

The Fate of Chromosomes and Alleles in an Allohexaploid Brassica Population

PubMed Central

Mason, Annaliese S.; Nelson, Matthew N.; Takahira, Junko; Cowling, Wallace A.; Alves, Gustavo Moreira; Chaudhuri, Arkaprava; Chen, Ning; Ragu, Mohana E.; Dalton-Morgan, Jessica; Coriton, Olivier; Huteau, Virginie; Eber, Frédérique; Chèvre, Anne-Marie; Batley, Jacqueline

2014-01-01

Production of allohexaploid Brassica (2n = AABBCC) is a promising goal for plant breeders due to the potential for hybrid heterosis and useful allelic contributions from all three of the Brassica genomes present in the cultivated diploid (2n = AA, 2n = BB, 2n = CC) and allotetraploid (2n = AABB, 2n = AACC, and 2n = BBCC) crop species (canola, cabbages, mustards). We used high-throughput SNP molecular marker assays, flow cytometry, and fluorescent in situ hybridization (FISH) to characterize a population of putative allohexaploids derived from self-pollination of a hybrid from the novel cross (B. napus × B. carinata) × B. juncea to investigate whether fertile, stable allohexaploid Brassica can be produced. Allelic segregation in the A and C genomes generally followed Mendelian expectations for an F2 population, with minimal nonhomologous chromosome pairing. However, we detected no strong selection for complete 2n = AABBCC chromosome complements, with weak correlations between DNA content and fertility (r2 = 0.11) and no correlation between missing chromosomes or chromosome segments and fertility. Investigation of next-generation progeny resulting from one highly fertile F2 plant using FISH revealed general maintenance of high chromosome numbers but severe distortions in karyotype, as evidenced by recombinant chromosomes and putative loss/duplication of A- and C-genome chromosome pairs. Our results show promise for the development of meiotically stable allohexaploid lines, but highlight the necessity of selection for 2n = AABBCC karyotypes. PMID:24558262

The fate of chromosomes and alleles in an allohexaploid Brassica population.

PubMed

Mason, Annaliese S; Nelson, Matthew N; Takahira, Junko; Cowling, Wallace A; Alves, Gustavo Moreira; Chaudhuri, Arkaprava; Chen, Ning; Ragu, Mohana E; Dalton-Morgan, Jessica; Coriton, Olivier; Huteau, Virginie; Eber, Frédérique; Chèvre, Anne-Marie; Batley, Jacqueline

2014-05-01

Production of allohexaploid Brassica (2n = AABBCC) is a promising goal for plant breeders due to the potential for hybrid heterosis and useful allelic contributions from all three of the Brassica genomes present in the cultivated diploid (2n = AA, 2n = BB, 2n = CC) and allotetraploid (2n = AABB, 2n = AACC, and 2n = BBCC) crop species (canola, cabbages, mustards). We used high-throughput SNP molecular marker assays, flow cytometry, and fluorescent in situ hybridization (FISH) to characterize a population of putative allohexaploids derived from self-pollination of a hybrid from the novel cross (B. napus × B. carinata) × B. juncea to investigate whether fertile, stable allohexaploid Brassica can be produced. Allelic segregation in the A and C genomes generally followed Mendelian expectations for an F2 population, with minimal nonhomologous chromosome pairing. However, we detected no strong selection for complete 2n = AABBCC chromosome complements, with weak correlations between DNA content and fertility (r(2) = 0.11) and no correlation between missing chromosomes or chromosome segments and fertility. Investigation of next-generation progeny resulting from one highly fertile F2 plant using FISH revealed general maintenance of high chromosome numbers but severe distortions in karyotype, as evidenced by recombinant chromosomes and putative loss/duplication of A- and C-genome chromosome pairs. Our results show promise for the development of meiotically stable allohexaploid lines, but highlight the necessity of selection for 2n = AABBCC karyotypes.

Sub-lethal glyphosate exposure alters flowering phenology and causes transient male-sterility in Brassica spp

PubMed Central

2014-01-01

Background Herbicide resistance in weedy plant populations can develop through different mechanisms such as gene flow of herbicide resistance transgenes from crop species into compatible weedy species or by natural evolution of herbicide resistance or tolerance following selection pressure. Results from our previous studies suggest that sub-lethal levels of the herbicide glyphosate can alter the pattern of gene flow between glyphosate resistant Canola®, Brassica napus, and glyphosate sensitive varieties of B. napus and B. rapa. The objectives of this study were to examine the phenological and developmental changes that occur in Brassica crop and weed species following sub-lethal doses of the herbicides glyphosate and glufosinate. We examined several vegetative and reproductive traits of potted plants under greenhouse conditions, treated with sub-lethal herbicide sprays. Results Our results indicate that exposure of Brassica spp. to a sub-lethal dose of glyphosate results in altering flowering phenology and reproductive function. Flowering of all sensitive species was significantly delayed and reproductive function, specifically male fertility, was suppressed. Higher dosage levels typically contributed to an increase in the magnitude of phenotypic changes. Conclusions These results demonstrate that Brassica spp. plants that are exposed to sub-lethal doses of glyphosate could be subject to very different pollination patterns and an altered pattern of gene flow that would result from changes in the overlap of flowering phenology between species. Implications include the potential for increased glyphosate resistance evolution and spread in weedy communities exposed to sub-lethal glyphosate. PMID:24655547

Sub-lethal glyphosate exposure alters flowering phenology and causes transient male-sterility in Brassica spp.

PubMed

Londo, Jason Paul; McKinney, John; Schwartz, Matthew; Bollman, Mike; Sagers, Cynthia; Watrud, Lidia

2014-03-21

Herbicide resistance in weedy plant populations can develop through different mechanisms such as gene flow of herbicide resistance transgenes from crop species into compatible weedy species or by natural evolution of herbicide resistance or tolerance following selection pressure. Results from our previous studies suggest that sub-lethal levels of the herbicide glyphosate can alter the pattern of gene flow between glyphosate resistant Canola®, Brassica napus, and glyphosate sensitive varieties of B. napus and B. rapa. The objectives of this study were to examine the phenological and developmental changes that occur in Brassica crop and weed species following sub-lethal doses of the herbicides glyphosate and glufosinate. We examined several vegetative and reproductive traits of potted plants under greenhouse conditions, treated with sub-lethal herbicide sprays. Our results indicate that exposure of Brassica spp. to a sub-lethal dose of glyphosate results in altering flowering phenology and reproductive function. Flowering of all sensitive species was significantly delayed and reproductive function, specifically male fertility, was suppressed. Higher dosage levels typically contributed to an increase in the magnitude of phenotypic changes. These results demonstrate that Brassica spp. plants that are exposed to sub-lethal doses of glyphosate could be subject to very different pollination patterns and an altered pattern of gene flow that would result from changes in the overlap of flowering phenology between species. Implications include the potential for increased glyphosate resistance evolution and spread in weedy communities exposed to sub-lethal glyphosate.

Prospects for Classical Biological Control of Saharan Mustard (Brassica tournefortii)

USDA-ARS?s Scientific Manuscript database

Saharan mustard (Brassica tournefortii) is a winter annual plant that is native to the Mediterranean Basin and is becoming highly invasive in the Sonoran and Mojave Deserts and adjacent areas and has spread great distances along highways from its original infestation. It is becoming a serious probl...

Omics Approach to Identify Factors Involved in Brassica Disease Resistance.

PubMed

Francisco, Marta; Soengas, Pilar; Velasco, Pablo; Bhadauria, Vijai; Cartea, Maria E; Rodríguez, Victor M

2016-01-01

Understanding plant's defense mechanisms and their response to biotic stresses is of fundamental meaning for the development of resistant crop varieties and more productive agriculture. The Brassica genus involves a large variety of economically important species and cultivars used as vegetable source, oilseeds, forage and ornamental. Damage caused by pathogens attack affects negatively various aspects of plant growth, development, and crop productivity. Over the last few decades, advances in plant physiology, genetics, and molecular biology have greatly improved our understanding of plant responses to biotic stress conditions. In this regard, various 'omics' technologies enable qualitative and quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. In this review, we have described advances in 'omic' tools (genomics, transcriptomics, proteomics and metabolomics) in the view of conventional and modern approaches being used to elucidate the molecular mechanisms that underlie Brassica disease resistance.

Transcriptomic basis for drought-resistance in Brassica napus L.

NASA Astrophysics Data System (ADS)

Wang, Pei; Yang, Cuiling; Chen, Hao; Song, Chunpeng; Zhang, Xiao; Wang, Daojie

2017-01-01

Based on transcriptomic data from four experimental settings with drought-resistant and drought-sensitive cultivars under drought and well-watered conditions, statistical analysis revealed three categories encompassing 169 highly differentially expressed genes (DEGs) in response to drought in Brassica napus L., including 37 drought-resistant cultivar-related genes, 35 drought-sensitive cultivar-related genes and 97 cultivar non-specific ones. We provide evidence that the identified DEGs were fairly uniformly distributed on different chromosomes and their expression patterns are variety specific. Except commonly enriched in response to various stimuli or stresses, different categories of DEGs show specific enrichment in certain biological processes or pathways, which indicated the possibility of functional differences among the three categories. Network analysis revealed relationships among the 169 DEGs, annotated biological processes and pathways. The 169 DEGs can be classified into different functional categories via preferred pathways or biological processes. Some pathways might simultaneously involve a large number of shared DEGs, and these pathways are likely to cross-talk and have overlapping biological functions. Several members of the identified DEGs fit to drought stress signal transduction pathway in Arabidopsis thaliana. Finally, quantitative real-time PCR validations confirmed the reproducibility of the RNA-seq data. These investigations are profitable for the improvement of crop varieties through transgenic engineering.

Brassica napus Genome Possesses Extraordinary High Number of CAMTA Genes and CAMTA3 Contributes to PAMP Triggered Immunity and Resistance to Sclerotinia sclerotiorum

PubMed Central

Rahman, Hafizur; Xu, You-Ping; Zhang, Xuan-Rui; Cai, Xin-Zhong

2016-01-01

Calmodulin-binding transcription activators (CAMTAs) play important roles in various plant biological processes including disease resistance and abiotic stress tolerance. Oilseed rape (Brassica napus L.) is one of the most important oil-producing crops worldwide. To date, compositon of CAMTAs in genomes of Brassica species and role of CAMTAs in resistance to the devastating necrotrophic fungal pathogen Sclerotinia sclerotiorum are still unknown. In this study, 18 CAMTA genes were identified in oilseed rape genome through bioinformatics analyses, which were inherited from the nine copies each in its progenitors Brassica rapa and Brassica oleracea and represented the highest number of CAMTAs in a given plant species identified so far. Gene structure, protein domain organization and phylogentic analyses showed that the oilseed rape CAMTAs were structurally similar and clustered into three major groups as other plant CAMTAs, but had expanded subgroups CAMTA3 and CAMTA4 genes uniquely in rosids species occurring before formation of oilseed rape. A large number of stress response-related cis-elements existed in the 1.5 kb promoter regions of the BnCAMTA genes. BnCAMTA genes were expressed differentially in various organs and in response to treatments with plant hormones and the toxin oxalic acid (OA) secreted by S. sclerotiorum as well as the pathogen inoculation. Remarkably, the expression of BnCAMTA3A1 and BnCAMTA3C1 was drastically induced in early phase of S. sclerotiorum infection, indicating their potential role in the interactions between oilseed rape and S. sclerotiorum. Furthermore, inoculation analyses using Arabidopsis camta mutants demonstrated that Atcamta3 mutant plants exhibited significantly smaller disease lesions than wild-type and other Atcamta mutant plants. In addition, compared with wild-type plants, Atcamta3 plants accumulated obviously more hydrogen peroxide in response to the PAMP chitin and exhibited much higher expression of the CGCG

Molecular characterization of two genotypes of a new polerovirus infecting brassicas in China.

PubMed

Xiang, Hai-Ying; Dong, Shu-Wei; Shang, Qiao-Xia; Zhou, Cui-Ji; Li, Da-Wei; Yu, Jia-Lin; Han, Cheng-Gui

2011-12-01

The genomic RNA sequences of two genotypes of a brassica-infecting polerovirus from China were determined. Sequence analysis revealed that the virus was closely related to but significantly different from turnip yellows virus (TuYV). This virus and other poleroviruses, including TuYV, had less than 90% amino acid sequence identity in all gene products except the coat protein. Based on the molecular criterion (>10% amino acid sequence difference) for species demarcation in the genus Polerovirus, the virus represents a distinct species for which the name Brassica yellows virus (BrYV) is proposed. Interestingly, there were two genotypes of BrYV, which mainly differed in the 5'-terminal half of the genome.

Establishment of the biochemical and endocrine blood profiles in the Majorera and Palmera dairy goat breeds: the effect of feed restriction.

PubMed

Lérias, Joana R; Peña, Raquel; Hernández-Castellano, Lorenzo E; Capote, Juan; Castro, Noemí; Argüello, Anastasio; Araújo, Susana S; Saco, Yolanda; Bassols, Anna; Almeida, André M

2015-11-01

Feed restriction, and seasonal weight loss (SWL), are major setbacks for animal production in the tropics and the Mediterranean. They may be solved through the use of autochthonous breeds particularly well adapted to SWL. It is therefore of major importance to determine markers of tolerance to feed restriction of putative use in animal selection. Two indigenous breeds from the Canary Islands, Palmera and Majorera, are commonly used by dairy goat farmers and, interestingly, have different phenotype characteristics albeit with a common ancestry. Indeed, Majorera is well adapted to feed restriction whereas the Palmera is susceptible to feed restriction. In addition, regardless of their importance in dairy production, there are only a limited number of reports relating to these breeds and, to the best of our knowledge, there is no description of their blood metabolite standard values under control conditions or as affected by feed restriction. In this study we analysed the blood metabolite profiles in Majorera and Palmera goats aiming to establish the differential responses to feed restriction between the two breeds and to characterise their metabolite standard values under control conditions. We observed significant differences in creatinine, urea, non-esterified fatty acids (NEFAs), cholesterol, IGF-1 and T3 due to underfeeding. Furthermore, a PCA analysis, revealed that animals submitted to undernutrition could be distinguished from the control groups, with the formation of three separate clusters (Palmera individuals after 22 d of subnutrition (PE22); Majorera individuals after 22 d of subnutrition (ME22) and animals assigned to control conditions (MC0, MC22, PC0 and PC22)), highlighting different responses of the two breeds to undernutrition.

Feed intake limitation strategies for the growing rabbit: effect on feeding behaviour, welfare, performance, digestive physiology and health: a review.

PubMed

Gidenne, T; Combes, S; Fortun-Lamothe, L

2012-09-01

This review aims to present the different effects produced by a post-weaning intake limitation strategy on the growing rabbit, now largely used by French professional rabbit breeders. Although a quantitative feed restriction leads to slower growth, feed conversion (FC) is improved, particularly when the rabbits are again fed freely, as compensatory growth occurs. This better FC or the healthy rabbit is because of better digestion resulting from slower passage through the intestine, whereas the digestive physiology is slightly modified (morphometry of the intestinal mucosa, fermentation pattern, microbiota). Meat quality and carcass characteristics are not greatly affected by feed restriction, except for a lower dressing-out percentage. One of the main advantages of limiting post-weaning intake of the rabbit is to reduce the mortality and morbidity rate due to digestive disorders (particularly epizootic rabbit enteropathy syndrome). The consequences for animal welfare are debatable, as feed restriction probably leads to hunger, but it reduces the incidence of digestive troubles after weaning. However, the growing rabbit adapts very well to an intake limitation strategy, without any aggressive behaviour for congener. In conclusion, restriction strategies could improve profitability of rabbit breeding, but they should be adapted to any specific breeding situation, according to the national market, feed prices, etc.

Over-expression of miR158 causes pollen abortion in Brassica campestris ssp. chinensis.

PubMed

Ma, Zhiming; Jiang, Jianxia; Hu, Ziwei; Lyu, Tianqi; Yang, Yang; Jiang, Jingjing; Cao, Jiashu

2017-02-01

We identified and cloned the two precursors of miR158 and its target gene in Brassica campestris ssp. chinensis, which both had high relative expression in the inflorescences. Further study revealed that over-expression of miR158 caused reduced pollen varbility, which was caused by the degradation of pollen contents from the binucleate microspore stage. These results first suggest the role of miR158 in pollen development of Brassica campestris ssp. chinensis. MicroRNAs (miRNAs) play crucial roles in many important growth and development processes both in plants and animals by regulating the expression of their target genes via mRNA cleavage or translational repression. In this study, miR158, a Brassicaceae specific miRNA, was functionally characterized with regard to its role in pollen development of non-heading Chinese cabbage (Brassica campestris ssp. chinensis). Two family members of miR158 in B. campestris, namely bra-miR158a1 and bra-miR158a2, and their target gene bra027656, which encodes a pentatricopeptide repeat (PPR) containing protein, were identified. Then, qRT-PCR analysis and GUS-reporter system revealed that both bra-miR158 and its target gene had relatively high expression levels in the inflorescences. Further study revealed that over-expression of miR158 caused reduced pollen varbility and pollen germination ratio, and the degradation of pollen contents from the binucleate microspore stage was also found in those deformed pollen grains, which led to pollen shrinking and collapse in later pollen development stage. These results first shed light on the importance of miR158 in pollen development of Brassica campestris ssp. chinensis.

Improved Discrimination for Brassica Vegetables Treated with Agricultural Fertilizers Using a Combined Chemometric Approach.

PubMed

Yuan, Yuwei; Hu, Guixian; Chen, Tianjin; Zhao, Ming; Zhang, Yongzhi; Li, Yong; Xu, Xiahong; Shao, Shengzhi; Zhu, Jiahong; Wang, Qiang; Rogers, Karyne M

2016-07-20

Multielement and stable isotope (δ(13)C, δ(15)N, δ(2)H, δ(18)O, (207)Pb/(206)Pb, and (208)Pb/(206)Pb) analyses were combined to provide a new chemometric approach to improve the discrimination between organic and conventional Brassica vegetable production. Different combinations of organic and conventional fertilizer treatments were used to demonstrate this authentication approach using Brassica chinensis planted in experimental test pots. Stable isotope analyses (δ(15)N and δ(13)C) of B. chinensis using elemental analyzer-isotope ratio mass spectrometry easily distinguished organic and chemical fertilizer treatments. However, for low-level application fertilizer treatments, this dual isotope approach became indistinguishable over time. Using a chemometric approach (combined isotope and elemental approach), organic and chemical fertilizer mixes and low-level applications of synthetic and organic fertilizers were detectable in B. chinensis and their associated soils, improving the detection limit beyond the capacity of individual isotopes or elemental characterization. LDA shows strong promise as an improved method to discriminate genuine organic Brassica vegetables from produce treated with chemical fertilizers and could be used as a robust test for organic produce authentication.

Changes on protein expression associated with salinity tolerance in Brassica cell cultures.

PubMed

Martín, J P; Elavummoottil, O C; Moreno, M L

1993-09-01

The synthesis of proteins from salt-tolerant Brassica oleracea L. var. botrytis L. subvar. cauliflora (Gars.) DC. (cauliflower) cell cultures is modified in relation to controls in several features. There are nine newly induced polypeptides in tolerant cultures (absent in control conditions). Some of them are only present under low salt levels (85 mM NaCl). Another group seems to be representative of moderate and high salt levels (170 and 255 mM NaCl), and a third group is present in all the salt conditions tested. On the other hand, the synthesis of most of the polypeptides present in control conditions is modified in salt-tolerant cultures by increasing, decreasing or stopping their synthesis in any of the tested conditions. The relationship between these changes in Brassica and other plant systems is discussed.

Feeding Experimentation Device (FED): A flexible open-source device for measuring feeding behavior.

PubMed

Nguyen, Katrina P; O'Neal, Timothy J; Bolonduro, Olurotimi A; White, Elecia; Kravitz, Alexxai V

2016-07-15

Measuring food intake in rodents is a conceptually simple yet labor-intensive and temporally-imprecise task. Most commonly, food is weighed manually, with an interval of hours or days between measurements. Commercial feeding monitors are excellent, but are costly and require specialized caging and equipment. We have developed the Feeding Experimentation Device (FED): a low-cost, open-source, home cage-compatible feeding system. FED utilizes an Arduino microcontroller and open-source software and hardware. FED dispenses a single food pellet into a food well where it is monitored by an infrared beam. When the mouse removes the pellet, FED logs the timestamp to a secure digital (SD) card and dispenses a new pellet into the well. Post-hoc analyses of pellet retrieval timestamps reveal high-resolution details about feeding behavior. FED is capable of accurately measuring food intake, identifying discrete trends during light and dark-cycle feeding. Additionally, we show the utility of FED for measuring increases in feeding resulting from optogenetic stimulation of agouti-related peptide neurons in the arcuate nucleus of the hypothalamus. With a cost of ∼$350 per device, FED is >10× cheaper than commercially available feeding systems. FED is also self-contained, battery powered, and designed to be placed in standard colony rack cages, allowing for monitoring of true home cage feeding behavior. Moreover, FED is highly adaptable and can be synchronized with emerging techniques in neuroscience, such as optogenetics, as we demonstrate here. FED allows for accurate, precise monitoring of feeding behavior in a home cage setting. Published by Elsevier B.V.

Effects of microgravityon the structural organization of Brassica rapa photosynthetic appartus

NASA Astrophysics Data System (ADS)

Adamchuk, N.; Kordyum, E.; Guikema, J.

Leaf mesophyll cells of 13- and 15-day old Brassica rapa plants grown on board the space shuttle Columbia (STS-87) and in the ground control have been investigated using the methods of light and electron microscopy. 13-day old plants were fixed on orbit and 15-day old plants were fixed after landing. It was shown the essential differences in leaf mesophyll quantitative anatomical and ultrastructural characteristics between spaceflight and ground control variants. Both the volume of palisade parenchyma cells and a number of chloroplasts in those cells increased in spaceflight samples. Simultaneusly, a chloroplast size decreased together with increasing of a relative volume of stromal thylakoids, starch grains and plastoglobuli. It was also noted increasing of stromal thylakoid length. In the same time, both a total length of thylakoids in granae and the grana number diminished in space flight. In addition, the interthylakoid space could be expended and the thylakoid length was more variable in chloroplast granae on microgravity, that correlated with a shrinkage of thylakoids in granal stacks. The obtained data a er discussed with the questions on both the photosynthetic apparatus sensitivity to gravity and its adaptive possibility to microgravity.

Nitrous oxide emission factors for urine and dung from sheep fed either fresh forage rape (Brassica napus L.) or fresh perennial ryegrass (Lolium perenne L.).

PubMed

Luo, J; Sun, X Z; Pacheco, D; Ledgard, S F; Lindsey, S B; Hoogendoorn, C J; Wise, B; Watkins, N L

2015-03-01

In New Zealand, agriculture is predominantly based on pastoral grazing systems and animal excreta deposited on soil during grazing have been identified as a major source of nitrous oxide (N2O) emissions. Forage brassicas (Brassica spp.) have been increasingly used to improve lamb performance. Compared with conventional forage perennial ryegrass (Lolium perenne L.), a common forage in New Zealand, forage brassicas have faster growth rates, higher dry matter production and higher nutritive value. The aim of this study was to determine the partitioning of dietary nitrogen (N) between urine and dung in the excreta from sheep fed forage brassica rape (B. napus subsp. oleifera L.) or ryegrass, and then to measure N2O emissions when the excreta from the two different feed sources were applied to a pasture soil. A sheep metabolism study was conducted to determine urine and dung-N outputs from sheep fed forage rape or ryegrass, and N partitioning between urine and dung. Urine and dung were collected and then used in a field plot experiment for measuring N2O emissions. The experimental site contained a perennial ryegrass/white clover pasture on a poorly drained silt-loam soil. The treatments included urine from sheep fed forage rape or ryegrass, dung from sheep fed forage rape or ryegrass, and a control without dung or urine applied. N2O emission measurements were carried out using a static chamber technique. For each excreta type, the total N2O emissions and emission factor (EF3; N2O-N emitted during the 3- or 8-month measurement period as a per cent of animal urine or dung-N applied, respectively) were calculated. Our results indicate that, in terms of per unit of N intake, a similar amount of N was excreted in urine from sheep fed either forage rape or ryegrass, but less dung N was excreted from sheep fed forage rape than ryegrass. The EF3 for urine from sheep fed forage rape was lower compared with urine from sheep fed ryegrass. This may have been because of plant

Oxygen dependency of germinating Brassica seeds

NASA Astrophysics Data System (ADS)

Park, Myoung Ryoul; Hasenstein, Karl H.

2016-02-01

Establishing plants in space, Moon or Mars requires adaptation to altered conditions, including reduced pressure and composition of atmospheres. To determine the oxygen requirements for seed germination, we imbibed Brassica rapa seeds under varying oxygen concentrations and profiled the transcription patterns of genes related to early metabolism such as starch degradation, glycolysis, and fermentation. We also analyzed the activity of lactate dehydrogenase (LDH) and alcohol dehydrogenase (ADH), and measured starch degradation. Partial oxygen pressure (pO2) greater than 10% resulted in normal germination (i.e., protrusion of radicle about 18 hours after imbibition) but lower pO2 delayed and reduced germination. Imbibition in an oxygen-free atmosphere for three days resulted in no germination but subsequent transfer to air initiated germination in 75% of the seeds and the root growth rate was transiently greater than in roots germinated under ambient pO2. In hypoxic seeds soluble sugars degraded faster but the content of starch after 24 h was higher than at ambient oxygen. Transcription of genes related to starch degradation, α-amylase (AMY) and Sucrose Synthase (SUS), was higher under ambient O2 than under hypoxia. Glycolysis and fermentation pathway-related genes, glucose phosphate isomerase (GPI), 6-phosphofructokinase (PFK), fructose 1,6-bisphosphate aldolase (ALD), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), pyruvate decarboxylase (PDC), LDH, and ADH, were induced by low pO2. The activity of LDH and ADH was the highest in anoxic seeds. Germination under low O2 conditions initiated ethanolic fermentation. Therefore, sufficient oxygen availability is important for germination before photosynthesis provides necessary oxygen and the determination of an oxygen carrying capacity is important for uniform growth in space conditions.

Transcriptome profiling analysis reveals the role of silique in controlling seed oil content in Brassica napus.

PubMed

Huang, Ke-Lin; Zhang, Mei-Li; Ma, Guang-Jing; Wu, Huan; Wu, Xiao-Ming; Ren, Feng; Li, Xue-Bao

2017-01-01

Seed oil content is an important agronomic trait in oilseed rape. However, the molecular mechanism of oil accumulation in rapeseeds is unclear so far. In this report, RNA sequencing technique (RNA-Seq) was performed to explore differentially expressed genes in siliques of two Brassica napus lines (HFA and LFA which contain high and low oil contents in seeds, respectively) at 15 and 25 days after pollination (DAP). The RNA-Seq results showed that 65746 and 66033 genes were detected in siliques of low oil content line at 15 and 25 DAP, and 65236 and 65211 genes were detected in siliques of high oil content line at 15 and 25 DAP, respectively. By comparative analysis, the differentially expressed genes (DEGs) were identified in siliques of these lines. The DEGs were involved in multiple pathways, including metabolic pathways, biosynthesis of secondary metabolic, photosynthesis, pyruvate metabolism, fatty metabolism, glycophospholipid metabolism, and DNA binding. Also, DEGs were related to photosynthesis, starch and sugar metabolism, pyruvate metabolism, and lipid metabolism at different developmental stage, resulting in the differential oil accumulation in seeds. Furthermore, RNA-Seq and qRT-PCR data revealed that some transcription factors positively regulate seed oil content. Thus, our data provide the valuable information for further exploring the molecular mechanism of lipid biosynthesis and oil accumulation in B. nupus.

Transcriptome profiling analysis reveals the role of silique in controlling seed oil content in Brassica napus

PubMed Central

Huang, Ke-Lin; Zhang, Mei-Li; Ma, Guang-Jing; Wu, Huan; Wu, Xiao-Ming; Ren, Feng

2017-01-01

Seed oil content is an important agronomic trait in oilseed rape. However, the molecular mechanism of oil accumulation in rapeseeds is unclear so far. In this report, RNA sequencing technique (RNA-Seq) was performed to explore differentially expressed genes in siliques of two Brassica napus lines (HFA and LFA which contain high and low oil contents in seeds, respectively) at 15 and 25 days after pollination (DAP). The RNA-Seq results showed that 65746 and 66033 genes were detected in siliques of low oil content line at 15 and 25 DAP, and 65236 and 65211 genes were detected in siliques of high oil content line at 15 and 25 DAP, respectively. By comparative analysis, the differentially expressed genes (DEGs) were identified in siliques of these lines. The DEGs were involved in multiple pathways, including metabolic pathways, biosynthesis of secondary metabolic, photosynthesis, pyruvate metabolism, fatty metabolism, glycophospholipid metabolism, and DNA binding. Also, DEGs were related to photosynthesis, starch and sugar metabolism, pyruvate metabolism, and lipid metabolism at different developmental stage, resulting in the differential oil accumulation in seeds. Furthermore, RNA-Seq and qRT-PCR data revealed that some transcription factors positively regulate seed oil content. Thus, our data provide the valuable information for further exploring the molecular mechanism of lipid biosynthesis and oil accumulation in B. nupus. PMID:28594951

Wavelet multiresolution analyses adapted for the fast solution of boundary value ordinary differential equations

NASA Technical Reports Server (NTRS)

Jawerth, Bjoern; Sweldens, Wim

1993-01-01

We present ideas on how to use wavelets in the solution of boundary value ordinary differential equations. Rather than using classical wavelets, we adapt their construction so that they become (bi)orthogonal with respect to the inner product defined by the operator. The stiffness matrix in a Galerkin method then becomes diagonal and can thus be trivially inverted. We show how one can construct an O(N) algorithm for various constant and variable coefficient operators.

Influence of Light and Temperature on Gene Expression Leading to Accumulation of Specific Flavonol Glycosides and Hydroxycinnamic Acid Derivatives in Kale (Brassica oleracea var. sabellica).

PubMed

Neugart, Susanne; Krumbein, Angelika; Zrenner, Rita

2016-01-01

Light intensity and temperature are very important signals for the regulation of plant growth and development. Plants subjected to less favorable light or temperature conditions often respond with accumulation of secondary metabolites. Some of these metabolites have been identified as bioactive compounds, considered to exert positive effects on human health when consumed regularly. In order to test a typical range of growth parameters for the winter crop Brassica oleracea var. sabellica, plants were grown either at 400 μmol m(-2) s(-1) or 100 μmol m(-2) s(-1) at 10°C, or at 400 μmol m(-2) s(-1) with 5 or 15°C. The higher light intensity overall increased flavonol content of leaves, favoring the main quercetin glycosides, a caffeic acid monoacylated kaempferol triglycoside, and disinapoyl-gentiobiose. The higher temperature mainly increased the hydroxycinnamic acid derivative disinapoyl-gentiobiose, while at lower temperature synthesis is in favor of very complex sinapic acid acylated flavonol tetraglycosides such as kaempferol-3-O-sinapoyl-sophoroside-7-O-diglucoside. A global analysis of light and temperature dependent alterations of gene expression in B. oleracea var. sabellica leaves was performed with the most comprehensive Brassica microarray. When compared to the light experiment much less genes were differentially expressed in kale leaves grown at 5 or 15°C. A structured evaluation of differentially expressed genes revealed the expected enrichment in the functional categories of e.g. protein degradation at different light intensities or phytohormone metabolism at different temperature. Genes of the secondary metabolism namely phenylpropanoids are significantly enriched with both treatments. Thus, the genome of B. oleracea was screened for predicted genes putatively involved in the biosynthesis of flavonoids and hydroxycinnamic acid derivatives. All identified B. oleracea genes were analyzed for their most specific 60-mer oligonucleotides present on the

Influence of Light and Temperature on Gene Expression Leading to Accumulation of Specific Flavonol Glycosides and Hydroxycinnamic Acid Derivatives in Kale (Brassica oleracea var. sabellica)

PubMed Central

Neugart, Susanne; Krumbein, Angelika; Zrenner, Rita

2016-01-01

Light intensity and temperature are very important signals for the regulation of plant growth and development. Plants subjected to less favorable light or temperature conditions often respond with accumulation of secondary metabolites. Some of these metabolites have been identified as bioactive compounds, considered to exert positive effects on human health when consumed regularly. In order to test a typical range of growth parameters for the winter crop Brassica oleracea var. sabellica, plants were grown either at 400 μmol m−2 s−1 or 100 μmol m−2 s−1 at 10°C, or at 400 μmol m−2 s−1 with 5 or 15°C. The higher light intensity overall increased flavonol content of leaves, favoring the main quercetin glycosides, a caffeic acid monoacylated kaempferol triglycoside, and disinapoyl-gentiobiose. The higher temperature mainly increased the hydroxycinnamic acid derivative disinapoyl-gentiobiose, while at lower temperature synthesis is in favor of very complex sinapic acid acylated flavonol tetraglycosides such as kaempferol-3-O-sinapoyl-sophoroside-7-O-diglucoside. A global analysis of light and temperature dependent alterations of gene expression in B. oleracea var. sabellica leaves was performed with the most comprehensive Brassica microarray. When compared to the light experiment much less genes were differentially expressed in kale leaves grown at 5 or 15°C. A structured evaluation of differentially expressed genes revealed the expected enrichment in the functional categories of e.g. protein degradation at different light intensities or phytohormone metabolism at different temperature. Genes of the secondary metabolism namely phenylpropanoids are significantly enriched with both treatments. Thus, the genome of B. oleracea was screened for predicted genes putatively involved in the biosynthesis of flavonoids and hydroxycinnamic acid derivatives. All identified B. oleracea genes were analyzed for their most specific 60-mer oligonucleotides present on the

Adaptive single-pixel imaging with aggregated sampling and continuous differential measurements

NASA Astrophysics Data System (ADS)

Huo, Yaoran; He, Hongjie; Chen, Fan; Tai, Heng-Ming

2018-06-01

This paper proposes an adaptive compressive imaging technique with one single-pixel detector and single arm. The aggregated sampling (AS) method enables the reduction of resolutions of the reconstructed images. It aims to reduce the time and space consumption. The target image with a resolution up to 1024 × 1024 can be reconstructed successfully at the 20% sampling rate. The continuous differential measurement (CDM) method combined with a ratio factor of significant coefficient (RFSC) improves the imaging quality. Moreover, RFSC reduces the human intervention in parameter setting. This technique enhances the practicability of single-pixel imaging with the benefits from less time and space consumption, better imaging quality and less human intervention.

Locally adapted fish populations maintain small-scale genetic differentiation despite perturbation by a catastrophic flood event

PubMed Central

2010-01-01

Background Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae) in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs) drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence) were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration) before and after the flood. Results Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave), but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre). By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre. Conclusions The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little affected by temporary

Locally adapted fish populations maintain small-scale genetic differentiation despite perturbation by a catastrophic flood event.

PubMed

Plath, Martin; Hermann, Bernd; Schröder, Christiane; Riesch, Rüdiger; Tobler, Michael; García de León, Francisco J; Schlupp, Ingo; Tiedemann, Ralph

2010-08-23

Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae) in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs) drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence) were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration) before and after the flood. Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave), but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre). By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre. The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little affected by temporary perturbations, as adaptations

Adapted physical exercise enhances activation and differentiation potential of satellite cells in the skeletal muscle of old mice.

PubMed

Cisterna, Barbara; Giagnacovo, Marzia; Costanzo, Manuela; Fattoretti, Patrizia; Zancanaro, Carlo; Pellicciari, Carlo; Malatesta, Manuela

2016-05-01

During ageing, a progressive loss of skeletal muscle mass and a decrease in muscle strength and endurance take place, in the condition termed sarcopenia. The mechanisms of sarcopenia are complex and still unclear; however, it is known that muscle atrophy is associated with a decline in the number and/or efficiency of satellite cells, the main contributors to muscle regeneration. Physical exercise proved beneficial in sarcopenia; however, knowledge of the effect of adapted physical exercise on the myogenic properties of satellite cells in aged muscles is limited. In this study the amount and activation state of satellite cells as well as their proliferation and differentiation potential were assessed in situ by morphology, morphometry and immunocytochemistry at light and transmission electron microscopy on 28-month-old mice submitted to adapted aerobic physical exercise on a treadmill. Sedentary age-matched mice served as controls, and sedentary adult mice were used as a reference for an unperturbed control at an age when the capability of muscle regeneration is still high. The effect of physical exercise in aged muscles was further analysed by comparing the myogenic potential of satellite cells isolated from old running and old sedentary mice using an in vitro system that allows observation of the differentiation process under controlled experimental conditions. The results of this ex vivo and in vitro study demonstrated that adapted physical exercise increases the number and activation of satellite cells as well as their capability to differentiate into structurally and functionally correct myotubes (even though the age-related impairment in myotube formation is not fully reversed): this evidence further supports adapted physical exercise as a powerful, non-pharmacological approach to counteract sarcopenia and the age-related deterioration of satellite cell capabilities even at very advanced age. © 2016 Anatomical Society.

Simple Adaptive Single Differential Coherence Detection of BPSK Signals in IEEE 802.15.4 Wireless Sensor Networks

PubMed Central

Wen, Hong; Wang, Longye; Xie, Ping; Song, Liang; Tang, Jie; Liao, Runfa

2017-01-01

In this paper, we propose an adaptive single differential coherent detection (SDCD) scheme for the binary phase shift keying (BPSK) signals in IEEE 802.15.4 Wireless Sensor Networks (WSNs). In particular, the residual carrier frequency offset effect (CFOE) for differential detection is adaptively estimated, with only linear operation, according to the changing channel conditions. It was found that the carrier frequency offset (CFO) and chip signal-to-noise ratio (SNR) conditions do not need a priori knowledge. This partly benefits from that the combination of the trigonometric approximation sin−1(x)≈x and a useful assumption, namely, the asymptotic or high chip SNR, is considered for simplification of the full estimation scheme. Simulation results demonstrate that the proposed algorithm can achieve an accurate estimation and the detection performance can completely meet the requirement of the IEEE 802.15.4 standard, although with a little loss of reliability and robustness as compared with the conventional optimal single-symbol detector. PMID:29278404

Simple Adaptive Single Differential Coherence Detection of BPSK Signals in IEEE 802.15.4 Wireless Sensor Networks.

PubMed

Zhang, Gaoyuan; Wen, Hong; Wang, Longye; Xie, Ping; Song, Liang; Tang, Jie; Liao, Runfa

2017-12-26

In this paper, we propose an adaptive single differential coherent detection (SDCD) scheme for the binary phase shift keying (BPSK) signals in IEEE 802.15.4 Wireless Sensor Networks (WSNs). In particular, the residual carrier frequency offset effect (CFOE) for differential detection is adaptively estimated, with only linear operation, according to the changing channel conditions. It was found that the carrier frequency offset (CFO) and chip signal-to-noise ratio (SNR) conditions do not need a priori knowledge. This partly benefits from that the combination of the trigonometric approximation sin - 1 ( x ) ≈ x and a useful assumption, namely, the asymptotic or high chip SNR, is considered for simplification of the full estimation scheme. Simulation results demonstrate that the proposed algorithm can achieve an accurate estimation and the detection performance can completely meet the requirement of the IEEE 802.15.4 standard, although with a little loss of reliability and robustness as compared with the conventional optimal single-symbol detector.

Functional characterization of a novel Brassica LEAFY homolog from Indian mustard: Expression pattern and gain-of-function studies.

PubMed

Dhakate, Priyanka; Tyagi, Shikha; Singh, Anupama; Singh, Anandita

2017-05-01

LEAFY plays a central role in regulation of flowering time and floral meristem identity in plants. Unfortunately, LFY function remains uncharacterized in agronomicaly important Brassicas. Herein, we illustrate fine-mapping of expression domains of LFY in 15 cultivars of 6 Brassica species and describe gain-of-function phenotypes in Arabidopsis and Brassica. We depict early flowering and altered fatty-acid composition in transgenic seed. The cDNA encoding BjuLFY (417aa) shared only 85% identity with reported homolog of B.juncea implying distinctness. Quantitative RT-PCR based coarse expression mapping of BjuLFY in tissue samples representing 3 time points at specific days after sowing (DAS), pre-flowering (30 DAS), flowering (75 DAS) and post-flowering (110 DAS), depicted an intense pulse of BjuLFY expression restricted to primary floral buds (75 DAS) which subsided in secondary floral buds (110 DAS); expression in root samples was also recorded implying neo-functionalization. Fine-mapping of expression during flowering confirmed tightly regulated LFY expression during early stages of bud development in 15 cultivars of 6 Brassica species implying functional conservation. Ectopic expression of BjuLFY in A. thaliana and B. juncea caused floral meristem defects and precocious flowering. B. juncea transgenics (T 1 ) over-expressing BjuLFY flowered 20days earlier produced normal flowers. GC-MS analysis of mature seed from Brassica transgenics showed an altered fatty-acid profile suggestive of seed maturation occurring at lower temperatures vis-à-vis control. Our findings implicate BjuLFY as a regulator of flowering in B. juncea and suggest its application in developing climate resilient crops. Copyright © 2017 Elsevier B.V. All rights reserved.

Morphological and genetic characterization of a new cytoplasmic male sterility system (oxa CMS) in stem mustard (Brassica juncea).

PubMed

Heng, Shuangping; Liu, Sansan; Xia, Chunxiu; Tang, HongYu; Xie, Fei; Fu, Tingdong; Wan, Zhengjie

2018-01-01

KEY MESSAGE: oxa CMS is a new cytoplasmic male sterility type in Brassica juncea. oxa CMS is a cytoplasmic male sterility (CMS) line that has been widely used in the production and cultivation of stem mustard in the southwestern China. In this study, different CMS-type specific mitochondrial markers were used to confirm that oxa CMS is distinct from the pol CMS, ogu CMS, nap CMS, hau CMS, tour CMS, Moricandia arvensis CMS, orf220-type CMS, etc., that have been previously reported in Brassica crops. Pollen grains of the oxa CMS line are sterile with a self-fertility rate of almost 0% and the sterility strain rate and sterility degree of oxa CMS is 100% due to a specific flower structure and flowering habit. Scanning electron microscopy revealed that most pollen grains in mature anthers of the oxa CMS line are empty, flat and deflated. Semi-thin section further showed that the abortive stage of anther development in oxa CMS is initiated at the late uninucleate stage. Abnormally vacuolated microspores caused male sterility in the oxa CMS line. This cytological study combined with marker-assisted selection showed that oxa CMS is a novel CMS type in stem mustard (Brassica juncea). Interestingly, the abortive stage of oxa CMS is later than those in other CMS types reported in Brassica crops, and there is no negative effect on the oxa CMS line growth period. This study demonstrated that this novel oxa CMS has a unique flower structure with sterile pollen grains at the late uninucleate stage. Our results may help to uncover the mechanism of oxa CMS in Brassica juncea.

Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.

PubMed

Jeong, Young-Min; Kim, Namshin; Ahn, Byung Ohg; Oh, Mijin; Chung, Won-Hyong; Chung, Hee; Jeong, Seongmun; Lim, Ki-Byung; Hwang, Yoon-Jung; Kim, Goon-Bo; Baek, Seunghoon; Choi, Sang-Bong; Hyung, Dae-Jin; Lee, Seung-Won; Sohn, Seong-Han; Kwon, Soo-Jin; Jin, Mina; Seol, Young-Joo; Chae, Won Byoung; Choi, Keun Jin; Park, Beom-Seok; Yu, Hee-Ju; Mun, Jeong-Hwan

2016-07-01

This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

Assessment of FAE1 polymorphisms in three Brassica species using EcoTILLING and their association with differences in seed erucic acid contents

PubMed Central

2010-01-01

Background FAE1 (fatty acid elongase1) is the key gene in the control of erucic acid synthesis in seeds of Brassica species. Due to oil with low erucic acid (LEA) content is essential for human health and not enough LEA resource could be available, thus new LEA genetic resources are being sought for Brassica breeding. EcoTILLING, a powerful genotyping method, can readily be used to identify polymorphisms in Brassica. Results Seven B. rapa, nine B. oleracea and 101 B. napus accessions were collected for identification of FAE1 polymorphisms. Three polymorphisms were detected in the two FAE1 paralogues of B. napus using EcoTILLING and were found to be strongly associated with differences in the erucic acid contents of seeds. In genomic FAE1 sequences obtained from seven B. rapa accessions, one SNP in the coding region was deduced to cause loss of gene function. Molecular evolution analysis of FAE1 homologues showed that the relationship between the Brassica A and C genomes is closer than that between the A/C genomes and Arabidopsis genome. Alignment of the coding sequences of these FAE1 homologues indicated that 18 SNPs differed between the A and C genomes and could be used as genome-specific markers in Brassica. Conclusion This study showed the applicability of EcoTILLING for detecting gene polymorphisms in Brassica. The association between B. napus FAE1 polymorphisms and the erucic acid contents of seeds may provide useful guidance for LEA breeding. The discovery of the LEA resource in B. rapa can be exploited in Brasscia cultivation. PMID:20594317

Assessment of FAE1 polymorphisms in three Brassica species using EcoTILLING and their association with differences in seed erucic acid contents.

PubMed

Wang, Nian; Shi, Lei; Tian, Fang; Ning, Huicai; Wu, Xiaoming; Long, Yan; Meng, Jinling

2010-07-01

FAE1 (fatty acid elongase1) is the key gene in the control of erucic acid synthesis in seeds of Brassica species. Due to oil with low erucic acid (LEA) content is essential for human health and not enough LEA resource could be available, thus new LEA genetic resources are being sought for Brassica breeding. EcoTILLING, a powerful genotyping method, can readily be used to identify polymorphisms in Brassica. Seven B. rapa, nine B. oleracea and 101 B. napus accessions were collected for identification of FAE1 polymorphisms. Three polymorphisms were detected in the two FAE1 paralogues of B. napus using EcoTILLING and were found to be strongly associated with differences in the erucic acid contents of seeds. In genomic FAE1 sequences obtained from seven B. rapa accessions, one SNP in the coding region was deduced to cause loss of gene function. Molecular evolution analysis of FAE1 homologues showed that the relationship between the Brassica A and C genomes is closer than that between the A/C genomes and Arabidopsis genome. Alignment of the coding sequences of these FAE1 homologues indicated that 18 SNPs differed between the A and C genomes and could be used as genome-specific markers in Brassica. This study showed the applicability of EcoTILLING for detecting gene polymorphisms in Brassica. The association between B. napus FAE1 polymorphisms and the erucic acid contents of seeds may provide useful guidance for LEA breeding. The discovery of the LEA resource in B. rapa can be exploited in Brasscia cultivation.

Responses of insect herbivores and their food plants to wind exposure and the importance of predation risk.

PubMed

Chen, Cong; Biere, Arjen; Gols, Rieta; Halfwerk, Wouter; van Oers, Kees; Harvey, Jeffrey A

2018-04-19

Wind is an important abiotic factor that influences an array of biological processes, but it is rarely considered in studies on plant-herbivore interactions. Here, we tested whether wind exposure could directly or indirectly affect the performance of two insect herbivores, Plutella xylostella and Pieris brassicae, feeding on Brassica nigra plants. In a greenhouse study using a factorial design, B. nigra plants were exposed to different wind regimes generated by fans before and after caterpillars were introduced on plants in an attempt to separate the effects of direct and indirect wind exposure on herbivores. Wind exposure delayed flowering, decreased plant height and increased leaf concentrations of amino acids and glucosinolates. Plant-mediated effects of wind on herbivores, that is effects of exposure of plants to wind prior to herbivore feeding, were generally small. However, development time of both herbivores was extended and adult body mass of P. xylostella was reduced when they were directly exposed to wind. By contrast, wind-exposed adult P. brassicae butterflies were significantly larger, revealing a trade-off between development time and adult size. Based on these results, we conducted a behavioural experiment to study preference by an avian predator, the great tit (Parus major) for last instar P. brassicae caterpillars on plants that were exposed to either control (no wind) or wind (fan-exposed) treatments. Tits captured significantly more caterpillars on still than on wind-exposed plants. Our results suggest that P. brassicae caterpillars are able to perceive the abiotic environment and to trade off the costs of extended development time against the benefits of increased size depending on the perceived risk of predation mediated by wind exposure. Such adaptive phenotypic plasticity in insects has not yet been described in response to wind exposure. © 2018 The Author. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of

Bentho-pelagic divergence of cichlid feeding architecture was prodigious and consistent during multiple adaptive radiations within African rift-lakes.

PubMed

Cooper, W James; Parsons, Kevin; McIntyre, Alyssa; Kern, Brittany; McGee-Moore, Alana; Albertson, R Craig

2010-03-08

How particular changes in functional morphology can repeatedly promote ecological diversification is an active area of evolutionary investigation. The African rift-lake cichlids offer a calibrated time series of the most dramatic adaptive radiations of vertebrate trophic morphology yet described, and the replicate nature of these events provides a unique opportunity to test whether common changes in functional morphology have repeatedly facilitated their ecological success. Specimens from 87 genera of cichlid fishes endemic to Lakes Tanganyka, Malawi and Victoria were dissected in order to examine the functional morphology of cichlid feeding. We quantified shape using geometric morphometrics and compared patterns of morphological diversity using a series of analytical tests. The primary axes of divergence were conserved among all three radiations, and the most prevalent changes involved the size of the preorbital region of the skull. Even the fishes from the youngest of these lakes (Victoria), which exhibit the lowest amount of skull shape disparity, have undergone extensive preorbital evolution relative to other craniofacial traits. Such changes have large effects on feeding biomechanics, and can promote expansion into a wide array of niches along a bentho-pelagic ecomorphological axis. Here we show that specific changes in trophic anatomy have evolved repeatedly in the African rift lakes, and our results suggest that simple morphological alterations that have large ecological consequences are likely to constitute critical components of adaptive radiations in functional morphology. Such shifts may precede more complex shape changes as lineages diversify into unoccupied niches. The data presented here, combined with observations of other fish lineages, suggest that the preorbital region represents an evolutionary module that can respond quickly to natural selection when fishes colonize new lakes. Characterizing the changes in cichlid trophic morphology that have

Nucleotide polymorphism affecting FLC expression underpins heading date variation in horticultural brassicas.

PubMed

Irwin, Judith A; Soumpourou, Eleni; Lister, Clare; Ligthart, Jan-Dick; Kennedy, Sue; Dean, Caroline

2016-09-01

Variation in flowering time and response to overwintering has been exploited to breed brassica vegetables that can be harvested year-round. Our knowledge of flowering time control now enables the investigation of the molecular basis of this important variation. Here, we show that a major determinant of heading date variation in Brassica oleracea is from variation in vernalization response through allelic variation at FLOWERING LOCUS C.C2 (BoFLC4). We characterize two alleles of BoFLC.C2 that are both functional and confer a requirement for vernalization, but they show distinct expression dynamics in response to cold. Complementation experiments in Arabidopsis thaliana revealed that the allelic variation results from cis polymorphism at BoFLC.C2, which quantitatively influences the degree of cold-induced epigenetic silencing. This results in one allelic variant conferring consistently later heading under both glasshouse and field conditions through reduced environmental sensitivity. Our results suggest that breeding of brassica varieties for commercially valuable variation in heading date has been achieved through the selection of cis polymorphism at FLC, similar to that underpinning natural variation in A. thaliana. This understanding will allow for the selection of alleles with distinct sensitivities to cold and robust heading dates under variable climatic conditions, and will facilitate the breeding of varieties more resistant to climate change. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

The green peach aphid Myzus persicae perform better on pre-infested Chinese cabbage Brassica pekinensis by enhancing host plant nutritional quality

PubMed Central

Cao, He-He; Liu, Hui-Ru; Zhang, Zhan-Feng; Liu, Tong-Xian

2016-01-01

The green peach aphid, Myzus persicae Sulzer, is a notorious pest on vegetables, which often aggregates in high densities on crop leaves. In this study, we investigated whether M. persicae could suppress the resistance level of Chinese cabbage Brassica pekinensis. M. persicae performed better in terms of weight gain (~33% increase) and population growth (~110% increase) when feeding on previously infested (pre-infested) Chinese cabbage compared with those on non-infested plants. However, when given a choice, 64% of the aphids preferred to settle on non-infested leaves, while 29% of aphids chose pre-infested leaves that had a 2.9 times higher concentration of glucosinolates. Aphid feeding significantly enhanced the amino acid:sugar ratio of phloem sap and the absolute amino acid concentration in plant leaves. Aphid infestation significantly increased the expression levels of salicylic acid (SA) marker genes, while it had marginal effects on the expression of jasmonate marker genes. Exogenously applied SA or methyl jasmonate had no significant effects on M. persicae performance, although these chemicals increased glucosinolates concentration in plant leaves. M. persicae infestation increase amino acid:sugar ratio and activate plant defenses, but aphid performed better on pre-infested plants, suggesting that both nutrition and toxics should be considered in insect-plant interaction. PMID:26905564

The better to eat you with: the comparative feeding morphology of phocid seals (Pinnipedia, Phocidae).

PubMed

Kienle, Sarah S; Berta, Annalisa

2016-03-01

One adaptation crucial to the survival of mammalian lineages that secondarily transitioned from land to water environments was the ability to capture and consume prey underwater. Phocid seals have evolved diverse feeding strategies to feed in the marine environment, and the objectives of this study were to document the specialized feeding morphologies and identify feeding strategies used by extant phocids. This study used principal component analysis (PCA) to determine the major axes of diversification in the skull for all extant phocid taxa and the recently extinct Caribbean monk seal (n = 19). Prey data gathered from the literature and musculoskeletal data from dissections were included to provide a comprehensive description of each feeding strategy. Random Forest analysis was used to determine the morphological, ecological and phylogenetic variables that best described each feeding strategy. There is morphological evidence for four feeding strategies in phocids: filter; grip and tear; suction; and pierce feeding. These feeding strategies are supported by quantitative cranial and mandibular characters, dietary information, musculoskeletal data and, for some species, behavioral observations. Most phocid species are pierce feeders, using a combination of biting and suction to opportunistically catch prey. Grip and tear and filter feeding are specialized strategies with specific morphological adaptations. These unique adaptations have allowed leopard seals (Hydrurga leptonyx) and crabeater seals (Lobodon carcinophaga) to exploit novel ecological niches and prey types. This study provides the first cranial and mandibular morphological evidence for the use of specialized suction feeding in hooded seals (Cystophora cristata), northern elephant seals (Mirounga angustirostris) and southern elephant seals (Mirounga leonina). The most important variables in determining the feeding strategy of a given phocid species were cranial and mandibular shape, diet, and phylogeny

Characterisation of taste-active extracts from raw Brassica oleracea vegetables.

PubMed

Zabaras, Dimitrios; Roohani, Mahshid; Krishnamurthy, Raju; Cochet, Maeva; Delahunty, Conor M

2013-04-25

Chemical and sensory characterisation of whole and fractionated myrosinase-free extracts from selected Australian-grown, raw Brassica vegetables (broccoli, cauliflower, Brussels sprouts and red cabbage) was carried out to determine the contribution of key phytochemicals (i.e. glucosinolates, free sugars, phenolics) to the taste profiles of these vegetables. Glucosinolate (GS) and phenolic profiles were determined by liquid chromatography coupled with photodiode array detection and mass spectrometry. Ten glucosinolates (GS) were quantified across the vegetables investigated. Brussels sprouts (186.3 μg g(-1) FW) followed by broccoli (164.1 μg g(-1) FW) were found to contain the most GS. The phenolic profiles of all samples were dominated by hydroxycinnamic acid derivatives. As expected, red cabbage was the only vegetable with a significant anthocyanin signal (574.0 μg g(-1) FW). Red cabbage (26.7 mg g(-1) FW) and cauliflower (18.7 mg g(-1) FW) were found to contain a higher concentration of free sugars than Brussels sprouts (12.6 mg g(-1) FW) and broccoli (10.2 mg g(-1) FW). Descriptive sensory analysis of the whole extracts found sweetness (cauliflower and red cabbage sweeter than broccoli and Brussels sprouts) and bitterness (Brussels sprouts more bitter than others) as the most discriminating attributes. A hydrophilic fraction with sweetness, umami and saltiness as the main attributes was the most taste active fraction across all Brassica whole extracts. Sub-fractionation showed that this fraction was also bitter but the presence of sugars counteracted bitterness. Several components within each extract were found to contribute to the bitterness of whole Brassica extracts. The total and individual GS content alone could not explain the perceived bitterness of these extracts. Phenolics and/or other components are likely to be contributing to the bitterness associated with these vegetables.

The first genetic map of a synthesized allohexaploid Brassica with A, B and C genomes based on simple sequence repeat markers.

PubMed

Yang, S; Chen, S; Geng, X X; Yan, G; Li, Z Y; Meng, J L; Cowling, W A; Zhou, W J

2016-04-01

We present the first genetic map of an allohexaploid Brassica species, based on segregating microsatellite markers in a doubled haploid mapping population generated from a hybrid between two hexaploid parents. This study reports the first genetic map of trigenomic Brassica. A doubled haploid mapping population consisting of 189 lines was obtained via microspore culture from a hybrid H16-1 derived from a cross between two allohexaploid Brassica lines (7H170-1 and Y54-2). Simple sequence repeat primer pairs specific to the A genome (107), B genome (44) and C genome (109) were used to construct a genetic linkage map of the population. Twenty-seven linkage groups were resolved from 274 polymorphic loci on the A genome (109), B genome (49) and C genome (116) covering a total genetic distance of 3178.8 cM with an average distance between markers of 11.60 cM. This is the first genetic framework map for the artificially synthesized Brassica allohexaploids. The linkage groups represent the expected complement of chromosomes in the A, B and C genomes from the original diploid and tetraploid parents. This framework linkage map will be valuable for QTL analysis and future genetic improvement of a new allohexaploid Brassica species, and in improving our understanding of the genetic control of meiosis in new polyploids.

Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis

PubMed Central

2010-01-01

Background In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In this study, a genome-wide expression profiling approach (cDNA-AFLP), validated by quantitative real-time polymerase chain reaction (qPCR) were used to get insights into the role of differential gene expression on the ecological adaptation of the marine snail Littorina saxatilis. This gastropod displays two sympatric ecotypes (RB and SU) which are becoming one of the best studied systems for ecological speciation. Results Among the 99 transcripts shared between ecotypes, 12.12% showed significant differential expression. At least 4% of these transcripts still displayed significant differences after correction for multiple tests, highlighting that gene expression can differ considerably between subpopulations adapted to alternative habitats in the face of gene flow. One of the transcripts identified was Cytochrome c Oxidase subunit I (COI). In addition, 6 possible reference genes were validated to normalize and confirm this result using qPCR. α-Tubulin and histone H3.3 showed the more stable expression levels, being therefore chosen as the best option for normalization. The qPCR analysis confirmed a higher COI expression in SU individuals. Conclusions At least 4% of the transcriptome studied is being differentially expressed between ecotypes living in alternative habitats, even when gene flow is still substantial between ecotypes. We could identify a candidate transcript of such ecotype differentiation: Cytochrome c Oxidase Subunit I (COI), a mitochondrial gene involved in energy metabolism. Quantitative PCR was used to confirm the differences found in COI and its over-expression in the SU ecotype. Interestingly, COI is involved in the oxidative

Acceptance of health-promoting Brassica vegetables: the influence of taste perception, information and attitudes.

PubMed

Cox, David N; Melo, Lauro; Zabaras, Dimitrios; Delahunty, Conor M

2012-08-01

To investigate the relative importance of specific health knowledge and taste on acceptance of Brassica vegetables (broccoli, red and green cabbages, broccolini, cauliflower, Brussels sprouts). In a sample of adults all reporting medium-high physical activity (as a marker/control of health behaviour) and reporting either low (≤2 portions/d) or high (≥3 portions/d) vegetable intake, half of those with low vegetable consumption (Li group) and half of those with high vegetable consumption (Hi group) received cancer protection information, while the other half did not (Ln and Hn groups), before hedonic (9-point), perceived taste and flavour impact responses (100 mm scales) to samples of six Brassica vegetables were elicited. Additionally, attitudes towards foods for health, pleasure and reward, sociodemographics, intentions to consume the vegetables in the near future and recall of health information were also measured. Adult males and females (n 200) aged 18-55 years. Central location testing, Adelaide, Australia. Information groups Li and Hi reported specific cancer protection information knowledge, in contrast to Ln and Hn groups (P < 0·000). Information independently influenced responses to (the least liked) Brussels sprouts only. Multivariate regression analysis found sensory perception tended to predict liking and intentions to consume Brassica vegetables. For example, broccoli hedonics (adjusted R 2 = 0·37) were predicted (P < 0·05) by bitterness (β = -0·38), flavour (β = 0·31), sweetness (β = 0·17) and female gender (β = 0·19) and intentions to consume (adjusted R 2 = 0·20) were predicted (P < 0·05) by bitterness (β = -0·38), flavour (β = 0·24), female gender (β = 0·20) and vegetable intake (β = 0·14). Addressing taste dimensions (while retaining healthy compounds) may be more important than promoting health information in order to increase the popularity of Brassica vegetables.

Development of Brassica oleracea-nigra monosomic alien addition lines: genotypic, cytological and morphological analyses.

PubMed

Tan, Chen; Cui, Cheng; Xiang, Yi; Ge, Xianhong; Li, Zaiyun

2017-12-01

We report the development and characterization of Brassica oleracea - nigra monosomic alien addition lines (MAALs) to dissect the Brassica B genome. Brassica nigra (2n = 16, BB) represents the diploid Brassica B genome which carries many useful genes and traits for breeding but received limited studies. To dissect the B genome from B. nigra, the triploid F 1 hybrid (2n = 26, CCB) obtained previously from the cross B. oleracea var. alboglabra (2n = 18, CC) × B. nigra was used as the maternal parent and backcrossed successively to parental B. oleracea. The progenies in BC 1 to BC 3 generations were analyzed by the methods of FISH and SSR markers to screen the monosomic alien addition lines (MAALs) with each of eight different B-genome chromosomes added to C genome (2n = 19, CC + 1B 1-8 ), and seven different MAALs were established, except for the one with chromosome B2 which existed in one triple addition. Most of these MAALs were distinguishable morphologically from each other, as they expressed the characters from B. nigra differently and at variable extents. The alien chromosome remained unpaired as a univalent in 86.24% pollen mother cells at diakinesis or metaphase I, and formed a trivalent with two C-genome chromosomes in 13.76% cells. Transmission frequency of all the added chromosomes was far higher through the ovules (averagely 14.40%) than the pollen (2.64%). The B1, B4 and B5 chromosomes were transmitted by female at much higher rates (22.38-30.00%) than the other four (B3, B6, B7, B8) (5.04-8.42%). The MAALs should be valuable for exploiting the genome structure and evolution of B. nigra.

Colorless chlorophyll catabolites in senescent florets of broccoli (Brassica oleracea var. italica).

PubMed

Roiser, Matthias H; Müller, Thomas; Kräutler, Bernhard

2015-02-11

Typical postharvest storage of broccoli (Brassica oleracea var. italica) causes degreening of this common vegetable with visible loss of chlorophyll (Chl). As shown here, colorless Chl-catabolites are generated. In fresh extracts of degreening florets of broccoli, three colorless tetrapyrrolic Chl-catabolites accumulated and were detected by high performance liquid chromatography (HPLC): two "nonfluorescent" Chl-catabolites (NCCs), provisionally named Bo-NCC-1 and Bo-NCC-2, and a colorless 1,19-dioxobilin-type "nonfluorescent" Chl-catabolite (DNCC), named Bo-DNCC. Analysis by nuclear magnetic resonance spectroscopy and mass spectrometry of these three linear tetrapyrroles revealed their structures. In combination with a comparison of their HPL-chromatographic properties, this allowed their identification with three known catabolites from two other brassicacea, namely two NCCs from oil seed rape (Brassica napus) and a DNCC from degreened leaves of Arabidopsis thaliana.

Colorless Chlorophyll Catabolites in Senescent Florets of Broccoli (Brassica oleracea var. italica)

PubMed Central

2015-01-01

Typical postharvest storage of broccoli (Brassica oleracea var. italica) causes degreening of this common vegetable with visible loss of chlorophyll (Chl). As shown here, colorless Chl-catabolites are generated. In fresh extracts of degreening florets of broccoli, three colorless tetrapyrrolic Chl-catabolites accumulated and were detected by high performance liquid chromatography (HPLC): two “nonfluorescent” Chl-catabolites (NCCs), provisionally named Bo-NCC-1 and Bo-NCC-2, and a colorless 1,19-dioxobilin-type “nonfluorescent” Chl-catabolite (DNCC), named Bo-DNCC. Analysis by nuclear magnetic resonance spectroscopy and mass spectrometry of these three linear tetrapyrroles revealed their structures. In combination with a comparison of their HPL-chromatographic properties, this allowed their identification with three known catabolites from two other brassicacea, namely two NCCs from oil seed rape (Brassica napus) and a DNCC from degreened leaves of Arabidopsis thaliana. PMID:25620234

Cranial mechanics and feeding in Tyrannosaurus rex.

PubMed Central

Rayfield, Emily J.

2004-01-01

It has been suggested that the large theropod dinosaur Tyrannosaurus rex was capable of producing extremely powerful bite forces and resisting multi-directional loading generated during feeding. Contrary to this suggestion is the observation that the cranium is composed of often loosely articulated facial bones, although these bones may have performed a shock-absorption role. The structural analysis technique finite element analysis (FEA) is employed here to investigate the functional morphology and cranial mechanics of the T. rex skull. In particular, I test whether the skull is optimized for the resistance of large bi-directional feeding loads, whether mobile joints are adapted for the localized resistance of feeding-induced stress and strain, and whether mobile joints act to weaken or strengthen the skull overall. The results demonstrate that the cranium is equally adapted to resist biting or tearing forces and therefore the 'puncture-pull' feeding hypothesis is well supported. Finite-element-generated stress-strain patterns are consistent with T. rex cranial morphology: the maxilla-jugal suture provides a tensile shock-absorbing function that reduces localized tension yet 'weakens' the skull overall. Furthermore, peak compressive and shear stresses localize in the nasals rather than the fronto-parietal region as seen in Allosaurus, offering a reason why robusticity is commonplace in tyrannosaurid nasals. PMID:15306316

Differential Maternal Feeding Practices, Eating Self-Regulation, and Adiposity in Young Twins

PubMed Central

Tripicchio, Gina L.; Keller, Kathleen L.; Johnson, Cassandra; Pietrobelli, Angelo; Heo, Moonseong

2014-01-01

OBJECTIVE: Restrictive feeding is associated with childhood obesity; however, this could be due to other factors that drive children to overeat and parents to restrict (eg, child genetics). Using a twin design to better control for confounders, we tested differences in restrictive feeding within families in relation to differences in twins’ self-regulatory eating and weight status. METHODS: Sixty-four same-gender twin pairs (4–7 years old) were studied with their mothers. Child caloric compensation ability (COMPX% index) was assessed by using a laboratory-based protocol. The Child Feeding Questionnaire assessed mothers’ self-reported feeding styles toward each twin. Child BMI (kg/m2) and BMI z score were calculated by using measured weight and height; percent body fat and waist circumference were also assessed. Partial correlations examined within-twin pair differences in Child Feeding Questionnaire subscales in relation to within-twin pair differences in anthropometry and caloric compensation (COMPX%). RESULTS: Differences in maternal restriction were significantly associated with within-pair differences in child COMPX% and BMI z score. Mothers reported more restriction toward the heavier and more poorly compensating twin. Additionally, within-pair differences in parental pressure to eat were associated with significant differences in BMI z score, percent body fat, and waist circumference. Mothers were more pressuring toward the lighter twin. CONCLUSIONS: Mothers vary in their feeding practices, even among same-gender twin pairs, which might influence differences in adiposity. Future research needs to elucidate cause-and-effect and intervention implications regarding parental restriction and pressure-to-eat prompts. PMID:25311601

Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus

PubMed Central

2013-01-01

Background The fertile and sterile plants were derived from the self-pollinated offspring of the F1 hybrid between the novel restorer line NR1 and the Nsa CMS line in Brassica napus. To elucidate gene expression and regulation caused by the A and C subgenomes of B. napus, as well as the alien chromosome and cytoplasm from Sinapis arvensis during the development of young floral buds, we performed a genome-wide high-throughput transcriptomic sequencing for young floral buds of sterile and fertile plants. Results In this study, equal amounts of total RNAs taken from young floral buds of sterile and fertile plants were sequenced using the Illumina/Solexa platform. After filtered out low quality data, a total of 2,760,574 and 2,714,441 clean tags were remained in the two libraries, from which 242,163 (Ste) and 253,507 (Fer) distinct tags were obtained. All distinct sequencing tags were annotated using all possible CATG+17-nt sequences of the genome and transcriptome of Brassica rapa and those of Brassica oleracea as the reference sequences, respectively. In total, 3231 genes of B. rapa and 3371 genes of B. oleracea were detected with significant differential expression levels. GO and pathway-based analyses were performed to determine and further to understand the biological functions of those differentially expressed genes (DEGs). In addition, there were 1089 specially expressed unknown tags in Fer, which were neither mapped to B. oleracea nor to B. rapa, and these unique tags were presumed to arise basically from the added alien chromosome of S. arvensis. Fifteen genes were randomly selected and their expression levels were confirmed by quantitative RT-PCR, and fourteen of them showed consistent expression patterns with the digital gene expression (DGE) data. Conclusions A number of genes were differentially expressed between the young floral buds of sterile and fertile plants. Some of these genes may be candidates for future research on CMS in Nsa line, fertility

Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus.

PubMed

Yan, Xiaohong; Dong, Caihua; Yu, Jingyin; Liu, Wanghui; Jiang, Chenghong; Liu, Jia; Hu, Qiong; Fang, Xiaoping; Wei, Wenhui

2013-01-16

The fertile and sterile plants were derived from the self-pollinated offspring of the F1 hybrid between the novel restorer line NR1 and the Nsa CMS line in Brassica napus. To elucidate gene expression and regulation caused by the A and C subgenomes of B. napus, as well as the alien chromosome and cytoplasm from Sinapis arvensis during the development of young floral buds, we performed a genome-wide high-throughput transcriptomic sequencing for young floral buds of sterile and fertile plants. In this study, equal amounts of total RNAs taken from young floral buds of sterile and fertile plants were sequenced using the Illumina/Solexa platform. After filtered out low quality data, a total of 2,760,574 and 2,714,441 clean tags were remained in the two libraries, from which 242,163 (Ste) and 253,507 (Fer) distinct tags were obtained. All distinct sequencing tags were annotated using all possible CATG+17-nt sequences of the genome and transcriptome of Brassica rapa and those of Brassica oleracea as the reference sequences, respectively. In total, 3231 genes of B. rapa and 3371 genes of B. oleracea were detected with significant differential expression levels. GO and pathway-based analyses were performed to determine and further to understand the biological functions of those differentially expressed genes (DEGs). In addition, there were 1089 specially expressed unknown tags in Fer, which were neither mapped to B. oleracea nor to B. rapa, and these unique tags were presumed to arise basically from the added alien chromosome of S. arvensis. Fifteen genes were randomly selected and their expression levels were confirmed by quantitative RT-PCR, and fourteen of them showed consistent expression patterns with the digital gene expression (DGE) data. A number of genes were differentially expressed between the young floral buds of sterile and fertile plants. Some of these genes may be candidates for future research on CMS in Nsa line, fertility restoration and improved agronomic

Development and validation of a duplex real-time PCR assay for the simultaneous detection of three mustard species (Sinapis alba, Brassica nigra and Brassica juncea) in food.

PubMed

Palle-Reisch, Monika; Cichna-Markl, Margit; Hochegger, Rupert

2014-06-15

The paper presents a duplex real-time PCR assay for the simultaneous detection of three potentially allergenic mustard species commonly used in food: white mustard (Sinapis alba), black mustard (Brassica nigra) and brown mustard (Brassica juncea). White mustard is detected in the "green" and black/brown mustard in the "yellow" channel. The duplex real-time PCR assay does not show cross-reactivity with other Brassicaceae species including broccoli, cauliflower, radish and rapeseed. Low cross-reactivities (difference in the Ct value ⩾ 11.91 compared with the positive control) were obtained with cumin, fenugreek, ginger, rye and turmeric. When applying 500 ng DNA per PCR tube, the duplex real-time PCR assay allowed the detection of white, black and brown mustard in brewed model sausages down to a concentration of 5mg/kg in 10 out of 10 replicates. The duplex real-time PCR assay was applied to verify correct labelling of commercial foodstuffs. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sustainability of ruminant agriculture in the new context: feeding strategies and features of animal adaptability into the necessary holistic approach.

PubMed

Bocquier, F; González-García, E

2010-07-01

There are numerous recent studies highlighting sustainability problems for the development of ruminant production systems (RPS) while facing increasing human food necessities and global climate change. Despite the complexity of the context, in our view the main objectives of the ruminants' physiologist should be convergent for both industrialized (IC) and developing countries (DC) in a common and global strategy of advancing knowledge. In DC, this means improving the efficiency of RPS, taking into account the unique possibility of using rangelands. For IC settings, RPS should be revisited in terms of autonomy and environment- friendly feeding and managing practices. Assuming that competition for feed/food use is still a crucial criterion, future ruminant feeding systems (FeSyst) should preferably focus on lignocellulosic sources. According to biome distributions, and the recent increases in volumes of crop residues and their by-products, the annually renewed volumes of these biomasses are considerable. Therefore, we need to redesign our strategies for their efficient utilization at the local level. For this purpose, digestion processes and rumen functioning need to be better understood. The renewed vision of ruminal digestion through the reduction of greenhouse gas emissions is also a key aspect as it is an environmental demand that cannot be ignored. With regard to other ruminants' physiological functions, accumulated knowledge could be mobilized into an integrative approach that puts forward the adaptive capacities of animals to face variability in quantity and quality of supplied feeds. Basically, the reduction of inputs that were traditionally used to ensure FeSyst will need more flexible animals. In that sense, the concepts of homeostasis and teleophorhesis need to be updated and adapted to domestic species and breeds that were until now largely excluded from the dominant productive systems. In conclusion, a more holistic approach of research targets is

Analysis of salicylic acid-dependent pathways in Arabidopsis thaliana following infection with Plasmodiophora brassicae and the influence of salicylic acid on disease.

PubMed

Lovelock, David A; Šola, Ivana; Marschollek, Sabine; Donald, Caroline E; Rusak, Gordana; van Pée, Karl-Heinz; Ludwig-Müller, Jutta; Cahill, David M

2016-10-01

Salicylic acid (SA) biosynthesis, the expression of SA-related genes and the effect of SA on the Arabidopsis-Plasmodiophora brassicae interaction were examined. Biochemical analyses revealed that, in P. brassicae-infected Arabidopsis, the majority of SA is synthesized from chorismate. Real-time monitored expression of a gene for isochorismate synthase was induced on infection. SA can be modified after accumulation, either by methylation, improving its mobility, or by glycosylation, as one possible reaction for inactivation. Quantitative reverse transcription-polymerase chain reaction (qPCR) confirmed the induction of an SA methyltransferase gene, whereas SA glucosyltransferase expression was not changed after infection. Col-0 wild-type (wt) did not provide a visible phenotypic resistance response, whereas the Arabidopsis mutant dnd1, which constitutively activates the immune system, showed reduced gall scores. As dnd1 showed control of the pathogen, exogenous SA was applied to Arabidopsis in order to test whether it could suppress clubroot. In wt, sid2 (SA biosynthesis), NahG (SA-deficient) and npr1 (SA signalling-impaired) mutants, SA treatment did not alter the gall score, but positively affected the shoot weight. This suggests that SA alone is not sufficient for Arabidopsis resistance against P. brassicae. Semi-quantitative PCR revealed that wt, cpr1, dnd1 and sid2 showed elevated PR-1 expression on P. brassicae and SA + P. brassicae inoculation at 2 and 3 weeks post-inoculation (wpi), whereas NahG and npr1 showed no expression. This work contributes to the understanding of SA involvement in the Arabidopsis-P. brassicae interaction. © 2015 BSPP and John Wiley & Sons Ltd.

Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications.

PubMed

Yu, Jingyin; Tehrim, Sadia; Wang, Linhai; Dossa, Komivi; Zhang, Xiurong; Ke, Tao; Liao, Boshou

2017-09-18

The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in Brassica after splitting from a common ancestor with Arabidopsis thaliana. Using Hidden Markov Model search and manual curation, we detected that Brassica species have nearly 1.4-fold as many P450 members as A. thaliana. Most P450s in A. thaliana and Brassica species were located on pseudo-chromosomes. The inferred phylogeny indicated that all P450s were clustered into two different subgroups. Analysis of WGD event revealed that different P450 gene families had appeared after evolutionary events of species. For the TD event analyses, the P450s from TD events in Brassica species can be divided into ancient and recent parts. Our comparison of influence of WGD and TD events on the P450 gene superfamily between A. thaliana and Brassica species indicated that the family-specific evolution in the Brassica lineage can be attributed to both WGD and TD, whereas WGD was recognized as the major mechanism for the recent evolution of the P450 super gene family. Expression analysis of P450s from A. thaliana and Brassica species indicated that WGD-type P450s showed the same expression pattern but completely different expression with TD-type P450s across different tissues in Brassica species. Selection force analysis suggested that P450 orthologous gene pairs between A. thaliana and Brassica species underwent negative selection, but no significant differences were found between P450 orthologous gene pairs in A. thaliana-B. rapa and A. thaliana-B. oleracea lineages, as well as in different subgenomes in B. rapa or B. oleracea compared with A. thaliana. This study is the first to investigate the effects of WGD and TD on the evolutionary history and functional divergence of P450

Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

PubMed Central

Gehan, Malia A; Mockler, Todd C; Weinig, Cynthia; Ewers, Brent E

2017-01-01

The dynamics of local climates make development of agricultural strategies challenging. Yield improvement has progressed slowly, especially in drought-prone regions where annual crop production suffers from episodic aridity. Underlying drought responses are circadian and diel control of gene expression that regulate daily variations in metabolic and physiological pathways. To identify transcriptomic changes that occur in the crop Brassica rapa during initial perception of drought, we applied a co-expression network approach to associate rhythmic gene expression changes with physiological responses. Coupled analysis of transcriptome and physiological parameters over a two-day time course in control and drought-stressed plants provided temporal resolution necessary for correlation of network modules with dynamic changes in stomatal conductance, photosynthetic rate, and photosystem II efficiency. This approach enabled the identification of drought-responsive genes based on their differential rhythmic expression profiles in well-watered versus droughted networks and provided new insights into the dynamic physiological changes that occur during drought. PMID:28826479

Pollen recognition and rejection during the sporophytic self-incompatibility response: Brassica and beyond.

PubMed

Hiscock, Simon J; McInnis, Stephanie M

2003-12-01

Many hermaphrodite flowering plants avoid self-fertilization through genetic systems of self-incompatibility (SI). SI allows a plant to recognize and to reject self or self-related pollen, thereby preserving its ovules for outcrossing. Genes situated at the S-locus encode the 'male' (pollen) and 'female' (pistil) recognition determinants of SI. In sporophytic SI (SSI) the male determinant is expressed in the diploid anther, therefore haploid pollen grains behave with a diploid S phenotype. In Brassica, the male and the female determinants of SSI have been identified as a peptide ligand and its cognate receptor, respectively, and recent studies have identified downstream signalling molecules involved in pollen rejection. It now needs to be established whether the Brassica mechanism is universal in species with SSI, or unique to the Brassicaceae.

Performances of survival, feeding behavior, and gene expression in aphids reveal their different fitness to host alteration

PubMed Central

Lu, Hong; Yang, Pengcheng; Xu, Yongyu; Luo, Lan; Zhu, Junjie; Cui, Na; Kang, Le; Cui, Feng

2016-01-01

Insect populations feeding on different plant species are under selection pressure to adapt to these differences. A study integrating elements of the ecology, behavior, and gene expression of aphids on different host plants has not yet been well-explored. The present study explores the relationship between host fitness and survival, feeding behavior, and salivary gland gene expression of a pea (Pisum sativum) host race of Acyrthosiphon pisum feeding on a common host Vicia faba and on three genetically-related hosts (Vicia villosa, Medicago truncatula, and Medicago sativa). Life table data indicated that aphids on non-favored hosts exhibited small size, low reproduction rate, slow population increase and individual development, and long lifespan. Electrical penetration graph results showed that the aphids spent significantly less time in passive ingestion of phloem sap on all non-preferred host plants before acclimation. After a period of acclimation on M. truncatula and V. villosa, pea host race individuals showed improved feeding behavior. No individuals of the pea host race completed its life history on M. sativa. Interestingly, the number of host-specific differentially-expressed salivary gland genes was negatively correlated with the fitness of aphids on this host plant. This study provided important cues in host plant specialization in aphids. PMID:26758247

Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation

PubMed Central

2011-01-01

Background Phenotypic evolution and its role in the diversification of organisms is a central topic in evolutionary biology. A neglected factor during the modern evolutionary synthesis, adaptive phenotypic plasticity, more recently attracted the attention of many evolutionary biologists and is now recognized as an important ingredient in both population persistence and diversification. The traits and directions in which an ancestral source population displays phenotypic plasticity might partly determine the trajectories in morphospace, which are accessible for an adaptive radiation, starting from the colonization of a novel environment. In the case of repeated colonizations of similar environments from the same source population this "flexible stem" hypothesis predicts similar phenotypes to arise in repeated subsequent radiations. The Midas Cichlid (Amphilophus spp.) in Nicaragua has radiated in parallel in several crater-lakes seeded by populations originating from the Nicaraguan Great Lakes. Here, we tested phenotypic plasticity in the pharyngeal jaw of Midas Cichlids. The pharyngeal jaw apparatus of cichlids, a second set of jaws functionally decoupled from the oral ones, is known to mediate ecological specialization and often differs strongly between sister-species. Results We performed a common garden experiment raising three groups of Midas cichlids on food differing in hardness and calcium content. Analyzing the lower pharyngeal jaw-bones we find significant differences between diet groups qualitatively resembling the differences found between specialized species. Observed differences in pharyngeal jaw expression between groups were attributable to the diet's mechanical resistance, whereas surplus calcium in the diet was not found to be of importance. Conclusions The pharyngeal jaw apparatus of Midas Cichlids can be expressed plastically if stimulated mechanically during feeding. Since this trait is commonly differentiated - among other traits - between

Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation.

PubMed

Muschick, Moritz; Barluenga, Marta; Salzburger, Walter; Meyer, Axel

2011-04-30

Phenotypic evolution and its role in the diversification of organisms is a central topic in evolutionary biology. A neglected factor during the modern evolutionary synthesis, adaptive phenotypic plasticity, more recently attracted the attention of many evolutionary biologists and is now recognized as an important ingredient in both population persistence and diversification. The traits and directions in which an ancestral source population displays phenotypic plasticity might partly determine the trajectories in morphospace, which are accessible for an adaptive radiation, starting from the colonization of a novel environment. In the case of repeated colonizations of similar environments from the same source population this "flexible stem" hypothesis predicts similar phenotypes to arise in repeated subsequent radiations. The Midas Cichlid (Amphilophus spp.) in Nicaragua has radiated in parallel in several crater-lakes seeded by populations originating from the Nicaraguan Great Lakes. Here, we tested phenotypic plasticity in the pharyngeal jaw of Midas Cichlids. The pharyngeal jaw apparatus of cichlids, a second set of jaws functionally decoupled from the oral ones, is known to mediate ecological specialization and often differs strongly between sister-species. We performed a common garden experiment raising three groups of Midas cichlids on food differing in hardness and calcium content. Analyzing the lower pharyngeal jaw-bones we find significant differences between diet groups qualitatively resembling the differences found between specialized species. Observed differences in pharyngeal jaw expression between groups were attributable to the diet's mechanical resistance, whereas surplus calcium in the diet was not found to be of importance. The pharyngeal jaw apparatus of Midas Cichlids can be expressed plastically if stimulated mechanically during feeding. Since this trait is commonly differentiated--among other traits--between Midas Cichlid species, its plasticity

Effect of biofumigation with brassica pellets combined with Brassicaceae cover crops and plastic cover on the survival and infectivity of inoculum of Phytophthora nicotianae Breda de Haan.

PubMed

Rodríguez-Molina, M Carmen; Serrano-Pérez, Paula; Palo, Carolina

2016-07-01

Biofumigation with defatted seed meal of Brassicaceae in the form of pellets has several advantages over the incorporation of fresh Brassicaceae crops to control soil-borne diseases. Two field experiments were established to evaluate the effect of biofumigation with brassica pellets on the survival and infectivity of Phytophthora nicotianae Breda de Haan inoculum introduced before treatments. In the spring experiment the incorporation of additional Brassicaceae cover crop (Brassica nigra L. and Sinapis alba L.) was tested, and in the summer experiment two brassica pellet doses were applied. Biofumigation with brassica pellets in spring (3000 kg ha(-1) with and without plastic) or in summer (3000 kg ha(-1) with or without plastic; 6000 kg ha(-1) without plastic) had no significant effect on the survival of P. nicotianae, regardless of the incorporation of additional Brassicaceae cover crop in spring. Reduction in infectivity in spring was related to the application of plastic, especially when combined with brassica pellets and Brassicaceae crop. In summer, soil temperature was the main factor in the inactivation of the inoculum, especially when plastic was applied, and no additional inactivation was achieved with brassica pellets. In spring and summer, biofumigation with brassica pellets had no effect on the survival of P. nicotianae. Application of plastic in spring may reduce infectivity. Soil temperature is the main factor in the inactivation of inoculum in summer, especially when plastic is applied. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Concentrations of thiocyanate and goitrin in human plasma, their precursor concentrations in brassica vegetables, and associated potential risk for hypothyroidism

PubMed Central

Bunch, Ronald; Leung, Angela M.

2016-01-01

Brassica vegetables are common components of the diet and have beneficial as well as potentially adverse health effects. Following enzymatic breakdown, some glucosinolates in brassica vegetables produce sulforaphane, phenethyl, and indolylic isothiocyanates that possess anticarcinogenic activity. In contrast, progoitrin and indolylic glucosinolates degrade to goitrin and thiocyanate, respectively, and may decrease thyroid hormone production. Radioiodine uptake to the thyroid is inhibited by 194 μmol of goitrin, but not by 77 μmol of goitrin. Collards, Brussels sprouts, and some Russian kale (Brassica napus) contain sufficient goitrin to potentially decrease iodine uptake by the thyroid. However, turnip tops, commercial broccoli, broccoli rabe, and kale belonging to Brassica oleracae contain less than 10 μmol of goitrin per 100-g serving and can be considered of minimal risk. Using sulforaphane plasma levels following glucoraphanin ingestion as a surrogate for thiocyanate plasma concentrations after indole glucosinolate ingestion, the maximum thiocyanate contribution from indole glucosinolate degradation is estimated to be 10 μM, which is significantly lower than background plasma thiocyanate concentrations (40–69 μM). Thiocyanate generated from consumption of indole glucosinolate can be assumed to have minimal adverse risks for thyroid health. PMID:26946249

Humic Fertilizer and Vermicompost Applied to the Soil Can Positively Affect Population Growth Parameters of Trichogramma brassicae (Hymenoptera: Trichogrammatidae) on Eggs of Tuta absoluta (Lepidoptera: Gelechiidae).

PubMed

Mohamadi, P; Razmjou, J; Naseri, B; Hassanpour, M

2017-12-01

The tomato leaf miner, Tuta absoluta (Meyrick), is a devastating pest of tomato worldwide. One of the control measures of T. absoluta is the use of biological control agents, such as Trichogramma wasps. Interactions between natural enemies and insect pests may be affected by application of fertilizers, because changes in plant quality through the fertilizer application may therefore affect herbivore characteristics and suitability of them to parasitism. Laboratory tests were carried out to evaluate the life table parameters of Trichogramma brassicae Bezdenko on T. absoluta eggs reared on tomato plants treated either with vermicompost (40%), humic fertilizer (2 g/kg soil), or control (suitable mixture of field soil and sand). Population growth parameters of T. brassicae were affected by fertilizer treatments. Significant differences were found for immature life period and total fecundity of T. brassicae on the treatments. Differences of intrinsic rate of natural increase (r m ), finite rate of increase (λ), net reproductive rate (R 0 ), mean generation time (T), and doubling time (DT) of T. brassicae among treatments were also significant. The lowest values of r m , λ, and R 0 were recorded for T. brassicae developed on T. absoluta eggs on control treatment, whereas the highest values of these parameters were observed on 2 g/kg humic fertilizer. Furthermore, T. brassicae had the shortest T and DT values on 2 g/kg humic fertilizer and 40% vermicompost treatments. Our results showed that application of humic fertilizer and vermicompost could positively affect population growth parameters of T. brassicae on eggs of T. absoluta fed on tomato plants.

Finite-horizon differential games for missile-target interception system using adaptive dynamic programming with input constraints

NASA Astrophysics Data System (ADS)

Sun, Jingliang; Liu, Chunsheng

2018-01-01

In this paper, the problem of intercepting a manoeuvring target within a fixed final time is posed in a non-linear constrained zero-sum differential game framework. The Nash equilibrium solution is found by solving the finite-horizon constrained differential game problem via adaptive dynamic programming technique. Besides, a suitable non-quadratic functional is utilised to encode the control constraints into a differential game problem. The single critic network with constant weights and time-varying activation functions is constructed to approximate the solution of associated time-varying Hamilton-Jacobi-Isaacs equation online. To properly satisfy the terminal constraint, an additional error term is incorporated in a novel weight-updating law such that the terminal constraint error is also minimised over time. By utilising Lyapunov's direct method, the closed-loop differential game system and the estimation weight error of the critic network are proved to be uniformly ultimately bounded. Finally, the effectiveness of the proposed method is demonstrated by using a simple non-linear system and a non-linear missile-target interception system, assuming first-order dynamics for the interceptor and target.

Chromatic discrimination: differential contributions from two adapting fields

PubMed Central

Cao, Dingcai; Lu, Yolanda H.

2012-01-01

To test whether a retinal or cortical mechanism sums contributions from two adapting fields to chromatic discrimination, L/M discrimination was measured with a test annulus surrounded by an inner circular field and an outer rectangular field. A retinal summation mechanism predicted that the discrimination pattern would not change with a change in the fixation location. Therefore, the fixation was set either in the inner or the outer field in two experiments. When one of the adapting fields was “red” and the other was “green,” the adapting field where the observer fixated always had a stronger influence on chromatic discrimination. However, when one adapting field was “white” and the other was red or green, the white field always weighted more heavily than the other adapting field in determining discrimination thresholds, whether the white field or the fixation was in the inner or outer adapting field. These results suggest that a cortical mechanism determines the relative contributions from different adapting fields. PMID:22330364

Chromatic discrimination: differential contributions from two adapting fields.

PubMed

Cao, Dingcai; Lu, Yolanda H

2012-02-01

To test whether a retinal or cortical mechanism sums contributions from two adapting fields to chromatic discrimination, L/M discrimination was measured with a test annulus surrounded by an inner circular field and an outer rectangular field. A retinal summation mechanism predicted that the discrimination pattern would not change with a change in the fixation location. Therefore, the fixation was set either in the inner or the outer field in two experiments. When one of the adapting fields was "red" and the other was "green," the adapting field where the observer fixated always had a stronger influence on chromatic discrimination. However, when one adapting field was "white" and the other was red or green, the white field always weighted more heavily than the other adapting field in determining discrimination thresholds, whether the white field or the fixation was in the inner or outer adapting field. These results suggest that a cortical mechanism determines the relative contributions from different adapting fields. © 2012 Optical Society of America

Boundedness of the solutions for certain classes of fractional differential equations with application to adaptive systems.

PubMed

Aguila-Camacho, Norelys; Duarte-Mermoud, Manuel A

2016-01-01

This paper presents the analysis of three classes of fractional differential equations appearing in the field of fractional adaptive systems, for the case when the fractional order is in the interval α ∈(0,1] and the Caputo definition for fractional derivatives is used. The boundedness of the solutions is proved for all three cases, and the convergence to zero of the mean value of one of the variables is also proved. Applications of the obtained results to fractional adaptive schemes in the context of identification and control problems are presented at the end of the paper, including numerical simulations which support the analytical results. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Adaptive optics self-calibration using differential OTF (dOTF)

NASA Astrophysics Data System (ADS)

Rodack, Alexander T.; Knight, Justin M.; Codona, Johanan L.; Miller, Kelsey L.; Guyon, Olivier

2015-09-01

We demonstrate self-calibration of an adaptive optical system using differential OTF [Codona, JL; Opt. Eng. 0001; 52(9):097105-097105. doi:10.1117/1.OE.52.9.097105]. We use a deformable mirror (DM) along with science camera focal plane images to implement a closed-loop servo that both flattens the DM and corrects for non-common-path aberrations within the telescope. The pupil field modification required for dOTF measurement is introduced by displacing actuators near the edge of the illuminated pupil. Simulations were used to develop methods to retrieve the phase from the complex amplitude dOTF measurements for both segmented and continuous sheet MEMS DMs and tests were performed using a Boston Micromachines continuous sheet DM for verification. We compute the actuator correction updates directly from the phase of the dOTF measurements, reading out displacements and/or slopes at segment and actuator positions. Through simulation, we also explore the effectiveness of these techniques for a variety of photons collected in each dOTF exposure pair.

The Fate of Arabidopsis thaliana Homeologous CNSs and Their Motifs in the Paleohexaploid Brassica rapa

PubMed Central

Subramaniam, Sabarinath; Wang, Xiaowu; Freeling, Michael; Pires, J. Chris

2013-01-01

Following polyploidy, duplicate genes are often deleted, and if they are not, then duplicate regulatory regions are sometimes lost. By what mechanism is this loss and what is the chance that such a loss removes function? To explore these questions, we followed individual Arabidopsis thaliana–A. thaliana conserved noncoding sequences (CNSs) into the Brassica ancestor, through a paleohexaploidy and into Brassica rapa. Thus, a single Brassicaceae CNS has six potential orthologous positions in B. rapa; a single Arabidopsis CNS has three potential homeologous positions. We reasoned that a CNS, if present on a singlet Brassica gene, would be unlikely to lose function compared with a more redundant CNS, and this is the case. Redundant CNSs go nondetectable often. Using this logic, each mechanism of CNS loss was assigned a metric of functionality. By definition, proved deletions do not function as sequence. Our results indicated that CNSs that go nondetectable by base substitution or large insertion are almost certainly still functional (redundancy does not matter much to their detectability frequency), whereas those lost by inferred deletion or indels are approximately 75% likely to be nonfunctional. Overall, an average nondetectable, once-redundant CNS more than 30 bp in length has a 72% chance of being nonfunctional, and that makes sense because 97% of them sort to a molecular mechanism with “deletion” in its description, but base substitutions do cause loss. Similarly, proved-functional G-boxes go undetectable by deletion 82% of the time. Fractionation mutagenesis is a procedure that uses polyploidy as a mutagenic agent to genetically alter RNA expression profiles, and then to construct testable hypotheses as to the function of the lost regulatory site. We show fractionation mutagenesis to be a “deletion machine” in the Brassica lineage. PMID:23493633

Biofumigation for control of pale potato cyst nematodes: activity of brassica leaf extracts and green manures on Globodera pallida in vitro and in soil.

PubMed

Lord, James S; Lazzeri, Luca; Atkinson, Howard J; Urwin, Peter E

2011-07-27

The effects of brassica green manures on Globodera pallida were assessed in vitro and in soil microcosms. Twelve of 22 brassica accessions significantly inhibited the motility of G. pallida infective juveniles in vitro. Green manures of selected brassicas were then incorporated into soil containing encysted eggs of G. pallida. Their effect on egg viability was estimated by quantifying nematode actin 1 mRNA by RT-qPCR. The leaf glucosinolate profiles of the plants were determined by high-performance liquid chromatography. Three Brassica juncea lines (Nemfix, Fumus, and ISCI99) containing high concentrations of 2-propenyl glucosinolate were the most effective, causing over 95% mortality of encysted eggs of G. pallida in polyethylene-covered soil. The toxic effects of green manures were greater in polyethylene-covered than in open soil. Toxicity in soil correlated with the concentration of isothiocyanate-producing glucosinolate but not total glucosinolate in green manures.

Proteomic analysis of broccoli (Brassica oleracea) under high temperature and waterlogging stresses.

PubMed

Lin, Hsin-Hung; Lin, Kuan-Hung; Chen, Su-Ching; Shen, Yu-Hsing; Lo, Hsiao-Feng

2015-12-01

The production of broccoli (Brassica oleracea) is largely reduced by waterlogging and high temperature stresses. Heat-tolerant and heat-susceptible broccoli cultivars TSS-AVRDC-2 and B-75, respectively, were used for physiological and proteomic analyses. The objective of this study was to identify TSS-AVRDC-2 and B-75 proteins differentially regulated at different time periods in response to waterlogging at 40 °C for three days. TSS-AVRDC-2 exhibited significantly higher chlorophyll content, lower stomatal conductance, and better H 2 O 2 scavenging under stress in comparison to B-75. Two-dimensional liquid phase fractionation analyses revealed that Rubisco proteins in both varieties were regulated under stressing treatments, and that TSS-AVRDC-2 had higher levels of both Rubisco large and small subunit transcripts than B-75 when subjected to high temperature and/or waterlogging. This report utilizes physiological and proteomic approaches to discover changes in the protein expression profiles of broccoli in response to heat and waterlogging stresses. Higher levels of Rubisco proteins in TSS-AVRDC-2 could lead to increased carbon fixation efficiency to provide sufficient energy to enable stress tolerance under waterlogging at 40 °C.

The chromoplasts of Or mutants of cauliflower (Brassica oleracea L. var. botrytis).

PubMed

Paolillo, D J; Garvin, D F; Parthasarathy, M V

2004-12-01

The Or mutation in cauliflower (Brassica oleracea L. var. botrytis) leads to abnormal accumulations of beta-carotene in orange chromoplasts, in tissues in which leucoplasts are characteristic of wild-type plants. Or chromoplasts were investigated by light microscopy of fresh materials and electron microscopy of glutaraldehyde- and potassium permanganate-fixed materials. Carotenoid inclusions in Or chromoplasts resemble those found in carrot root chromoplasts in their optical activity and angular shape. Electron microscopy revealed that the inclusions are made up of parallel, membrane-bound compartments. These stacks of membranes are variously rolled and folded into three-dimensional objects. We classify Or chromoplasts as "membranous" chromoplasts. The Or mutation also limits plastid replication so that a single chromoplast constitutes the plastidome in most of the affected cells. There are one to two chromoplasts in each cell of a shoot apex. The ability of differentiated chromoplasts to divide in the apical meristems of Or mutant plants resembles the ability of proplastids to maintain plastid continuity from cell to cell in meristems of Arabidopsis thaliana mutants in which plastid replication is drastically limited. The findings are used to discuss the number of levels of regulation involved in plastid replication.

Differential response to stocking rates and feeding by two genotypes of Holstein-Friesian cows in a pasture-based automatic milking system.

PubMed

Nieman, C C; Steensma, K M; Rowntree, J E; Beede, D K; Utsumi, S A

2015-12-01

The throughput of automatic milking systems (AMS) is likely affected by differential traffic behavior and subsequent effects on the milking frequency and milk production of cows. This study investigated the effect of increasing stocking rate and partial mixed ration (PMR) on the milk production, dry matter intake (DMI), feed conversion efficiency (FCE) and use of AMS by two genotypes of Holstein-Friesian cows in mid-lactation. The study lasted 8 weeks and consisted in a factorial arrangement of two genotypes of dairy cattle, United States Holstein (USH) or New Zealand Friesian (NZF), and two pasture-based feeding treatments, a low stocking rate system (2 cows/ha) fed temperate pasture and concentrate, or a high stocking rate system (HSR; 3 cows/ha) fed same pasture and concentrate plus PMR. A total of 28 cows, 14 USH and 14 NZF, were used for comparisons, with 12 cows, six USH and six NZF, also used for tracking of animal movements. Data were analyzed by repeated measure mixed models for a completely randomized design. No differences (P>0.05) in pre- or post-grazing herbage mass, DMI and FCE were detected in response to increases in stocking rate and PMR feeding in HSR. However, there was a significant (P<0.05) grazing treatment×genotype×week interaction on milk production, explained by differential responses of genotypes to changes in herbage mass over time (P<0.001). A reduction (P<0.01) in hours spent on pasture was detected in response to PMR supplementation in HSR; this reduction was greater (P=0.01) for USH than NZF cows (6 v. 2 h, respectively). Regardless of the grazing treatment, USH cows had greater (P=0.02) milking frequency (2.51 v. 2.26±0.08 milkings/day) and greater (P<0.01) milk yield (27.3 v. 16.0±1.2 kg/day), energy-corrected milk (24.8 v. 16.5±1.0 kg/day), DMI (22.1 v. 16.6±0.8 kg/day) and FCE (1.25 v. 1.01±0.06 kg/kg) than NZF cows. There was also a different distribution of milkings/h between genotypes (P<0.001), with patterns of milkings

Differential flatness properties and adaptive control of the hypothalamic-pituitary-adrenal axis model

NASA Astrophysics Data System (ADS)

Rigatos, Gerasimos

2016-12-01

It is shown that the model of the hypothalamic-pituitary-adrenal gland axis is a differentially flat one and this permits to transform it to the so-called linear canonical form. For the new description of the system's dynamics the transformed control inputs contain unknown terms which depend on the system's parameters. To identify these terms an adaptive fuzzy approximator is used in the control loop. Thus an adaptive fuzzy control scheme is implemented in which the unknown or unmodeled system dynamics is approximated by neurofuzzy networks and next this information is used by a feedback controller that makes the state variables (CRH - corticotropin releasing hormone, adenocortocotropic hormone - ACTH, cortisol) of the hypothalamic-pituitary-adrenal gland axis model converge to the desirable levels (setpoints). This adaptive control scheme is exclusively implemented with the use of output feedback, while the state vector elements which are not directly measured are estimated with the use of a state observer that operates in the control loop. The learning rate of the adaptive fuzzy system is suitably computed from Lyapunov analysis, so as to assure that both the learning procedure for the unknown system's parameters, the dynamics of the observer and the dynamics of the control loop will remain stable. The performed Lyapunov stability analysis depends on two Riccati equations, one associated with the feedback controller and one associated with the state observer. Finally, it is proven that for the control scheme that comprises the feedback controller, the state observer and the neurofuzzy approximator, an H-infinity tracking performance can be succeeded.

Tuning growth cycles of Brassica crops via natural antisense transcripts of BrFLC.

PubMed

Li, Xiaorong; Zhang, Shaofeng; Bai, Jinjuan; He, Yuke

2016-03-01

Several oilseed and vegetable crops of Brassica are biennials that require a prolonged winter cold for flowering, a process called vernalization. FLOWERING LOCUS C (FLC) is a central repressor of flowering. Here, we report that the overexpression of natural antisense transcripts (NATs) of Brassica rapa FLC (BrFLC) greatly shortens plant growth cycles. In rapid-, medium- and slow-cycling crop types, there are four copies of the BrFLC genes, which show extensive variation in sequences and expression levels. In Bre, a biennial crop type that requires vernalization, five NATs derived from the BrFLC2 locus are rapidly induced under cold conditions, while all four BrFLC genes are gradually down-regulated. The transgenic Bre lines overexpressing a long NAT of BrFLC2 do not require vernalization, resulting in a gradient of shortened growth cycles. Among them, a subset of lines both flower and set seeds as early as Yellow sarson, an annual crop type in which all four BrFLC genes have non-sense mutations and are nonfunctional in flowering repression. Our results demonstrate that the growth cycles of biennial crops of Brassica can be altered by changing the expression levels of BrFLC2 NATs. Thus, BrFLC2 NATs and their transgenic lines are useful for the genetic manipulation of crop growth cycles. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Cranial mechanics and feeding in Tyrannosaurus rex.

PubMed

Rayfield, Emily J

2004-07-22

It has been suggested that the large theropod dinosaur Tyrannosaurus rex was capable of producing extremely powerful bite forces and resisting multi-directional loading generated during feeding. Contrary to this suggestion is the observation that the cranium is composed of often loosely articulated facial bones, although these bones may have performed a shock-absorption role. The structural analysis technique finite element analysis (FEA) is employed here to investigate the functional morphology and cranial mechanics of the T. rex skull. In particular, I test whether the skull is optimized for the resistance of large bi-directional feeding loads, whether mobile joints are adapted for the localized resistance of feeding-induced stress and strain, and whether mobile joints act to weaken or strengthen the skull overall. The results demonstrate that the cranium is equally adapted to resist biting or tearing forces and therefore the 'puncture-pull' feeding hypothesis is well supported. Finite-element-generated stress-strain patterns are consistent with T. rex cranial morphology: the maxilla-jugal suture provides a tensile shock-absorbing function that reduces localized tension yet 'weakens' the skull overall. Furthermore, peak compressive and shear stresses localize in the nasals rather than the fronto-parietal region as seen in Allosaurus, offering a reason why robusticity is commonplace in tyrannosaurid nasals. Copyright 2004 The Royal Society

Multi-element array signal reconstruction with adaptive least-squares algorithms

NASA Technical Reports Server (NTRS)

Kumar, R.

1992-01-01

Two versions of the adaptive least-squares algorithm are presented for combining signals from multiple feeds placed in the focal plane of a mechanical antenna whose reflector surface is distorted due to various deformations. Coherent signal combining techniques based on the adaptive least-squares algorithm are examined for nearly optimally and adaptively combining the outputs of the feeds. The performance of the two versions is evaluated by simulations. It is demonstrated for the example considered that both of the adaptive least-squares algorithms are capable of offsetting most of the loss in the antenna gain incurred due to reflector surface deformations.

The respective effects of soil heavy metal fractions by sequential extraction procedure and soil properties on the accumulation of heavy metals in rice grains and brassicas.

PubMed

Xiao, Ling; Guan, Dongsheng; Peart, M R; Chen, Yujuan; Li, Qiqi

2017-01-01

This study was carried out to examine heavy metal accumulation in rice grains and brassicas and to identify the different controls, such as soil properties and soil heavy metal fractions obtained by the Community Bureau of Reference (BCR) sequential extraction, in their accumulation. In Guangdong Province, South China, rice grain and brassica samples, along with their rhizospheric soil, were collected from fields on the basis of distance downstream from electroplating factories, whose wastewater was used for irrigation. The results showed that long-term irrigation using the electroplating effluent has not only enriched the rhizospheric soil with Cd, Cr, Cu, and Zn but has also increased their mobility and bioavailability. The average concentrations of Cd and Cr in rice grains and brassicas from closest to the electroplating factories were significantly higher than those from the control areas. Results from hybrid redundancy analysis (hRDA) and redundancy analysis (RDA) showed that the BCR fractions of soil heavy metals could explain 29.0 and 46.5 % of total eigenvalue for heavy metal concentrations in rice grains and brassicas, respectively, while soil properties could only explain 11.1 and 33.4 %, respectively. This indicated that heavy metal fractions exerted more control upon their concentrations in rice grains and brassicas than soil properties. In terms of metal interaction, an increase of residual Zn in paddy soil or a decrease of acid soluble Cd in the brassica soil could enhance the accumulation of Cd, Cu, Cr, and Pb in both rice grains and brassicas, respectively, while the reducible or oxidizable Cd in soil could enhance the plants' accumulation of Cr and Pb. The RDA showed an inhibition effect of sand content and CFO on the accumulation of heavy metals in rice grains and brassicas. Moreover, multiple stepwise linear regression could offer prediction for Cd, Cu, Cr, and Zn concentrations in the two crops by soil heavy metal fractions and soil properties.

Differential Responses of Two Broccoli (Brassica oleracea L. var Italica) Cultivars to Salinity and Nutritional Quality Improvement

PubMed Central

Zaghdoud, Chokri; Alcaraz-López, Carlos; Mota-Cadenas, César; Martínez-Ballesta, María del Carmen; Moreno, Diego A.; Ferchichi, Ali; Carvajal, Micaela

2012-01-01

The comparative responses of two broccoli cultivars (Brassica oleracea var. Italica, cv. Parthenon and cv. Naxos) to a 15 d exposure to different NaCl levels were investigated. Salinity led to increased concentrations of Na+ and Cl− ions in both cultivars, a disruption of the endogenous minerals levels in the shoots and roots—that varied with the cultivar and salt concentration—and decreases in the osmotic potential (Ψπ), root hydraulic conductance (L 0), and stomatal conductance (G s). The reduced biomass of Naxos at moderate NaCl indicates greater sensitivity to salinity, compared with Parthenon. Parthenon accumulated more soluble sugars, for osmotic adjustment, whereas Naxos accumulated proline, which gave the two cultivars differing nutritional characteristics. The total glucosinolates (GSLs) content was not affected by salinity in Parthenon while it decreased significantly in Naxos as a consequence of the decrease in the indole GSL. However, Naxos accumulated more aliphatic GSLs under salt stress than Parthenon, which confers on this cultivar a greater nutritional value when cultivated under salinity.These results suggest that, at distinct salinity levels, each broccoli cultivar adopts a specific strategy, indicating the crucial role of the genetic background on the organoleptic and nutritional properties that each cultivar acquires. PMID:22956893

Differential responses of two broccoli (Brassica oleracea L. var Italica) cultivars to salinity and nutritional quality improvement.

PubMed

Zaghdoud, Chokri; Alcaraz-López, Carlos; Mota-Cadenas, César; Martínez-Ballesta, María del Carmen; Moreno, Diego A; Ferchichi, Ali; Carvajal, Micaela

2012-01-01

The comparative responses of two broccoli cultivars (Brassica oleracea var. Italica, cv. Parthenon and cv. Naxos) to a 15 d exposure to different NaCl levels were investigated. Salinity led to increased concentrations of Na(+) and Cl(-) ions in both cultivars, a disruption of the endogenous minerals levels in the shoots and roots-that varied with the cultivar and salt concentration-and decreases in the osmotic potential (Ψ(π)), root hydraulic conductance (L(0)), and stomatal conductance (G(s)). The reduced biomass of Naxos at moderate NaCl indicates greater sensitivity to salinity, compared with Parthenon. Parthenon accumulated more soluble sugars, for osmotic adjustment, whereas Naxos accumulated proline, which gave the two cultivars differing nutritional characteristics. The total glucosinolates (GSLs) content was not affected by salinity in Parthenon while it decreased significantly in Naxos as a consequence of the decrease in the indole GSL. However, Naxos accumulated more aliphatic GSLs under salt stress than Parthenon, which confers on this cultivar a greater nutritional value when cultivated under salinity.These results suggest that, at distinct salinity levels, each broccoli cultivar adopts a specific strategy, indicating the crucial role of the genetic background on the organoleptic and nutritional properties that each cultivar acquires.

Role of Streptomyces pactum in phytoremediation of trace elements by Brassica juncea in mine polluted soils.

PubMed

Ali, Amjad; Guo, Di; Mahar, Amanullah; Wang, Zhen; Muhammad, Dost; Li, Ronghua; Wang, Ping; Shen, Feng; Xue, Quanhong; Zhang, Zengqiang

2017-10-01

The industrial expansion, smelting, mining and agricultural practices have increased the release of toxic trace elements (TEs) in the environment and threaten living organisms. The microbe-assisted phytoremediation is environmentally safe and provide an effective approach to remediate TEs contaminated soils. A pot experiment was conducted to test the potential of an Actinomycete, subspecies Streptomyces pactum (Act12) along with medical stone compost (MSC) by growing Brassica juncea in smelter and mines polluted soils of Feng County (FC) and Tongguan (TG, China), respectively. Results showed that Zn (7, 28%), Pb (54, 21%), Cd (16, 17%) and Cu (8, 10%) uptake in shoot and root of Brassica juncea was pronounced in FC soil. Meanwhile, the Zn (40, 14%) and Pb (82, 15%) uptake in the shoot and root were also increased in TG soil. Shoot Cd uptake remained below detection, while Cu decreased by 52% in TG soil. The Cd and Cu root uptake were increased by 17% and 33%, respectively. Results showed that TEs uptake in shoot increased with increasing Act12 dose. Shoot/root dry biomass, chlorophyll and carotenoid content in Brassica juncea were significantly influenced by the application of Act12 in FC and TG soil. The antioxidant enzymatic activities (POD, PAL, PPO and CAT) in Brassica juncea implicated enhancement in the plant defense mechanism against the TEs induced stress in contaminated soils. The extraction potential of Brasssica was further evaluated by TF (translocation factor) and MEA (metal extraction amount). Based on our findings, further investigation of Act12 assisted phytoremediation of TEs in the smelter and mines polluted soil and hyperaccumulator species are suggested for future studies. Copyright © 2017. Published by Elsevier Inc.

Introgression of Black Rot Resistance from Brassica carinata to Cauliflower (Brassica oleracea botrytis Group) through Embryo Rescue

PubMed Central

Sharma, Brij B.; Kalia, Pritam; Singh, Dinesh; Sharma, Tilak R.

2017-01-01

Black rot caused by Xanthomonas campestris pv. campestris (Xcc) is a very important disease of cauliflower (Brassica oleracea botrytis group) resulting into 10–50% yield losses every year. Since there is a dearth of availability of resistance to black rot disease in B. oleracea (C genome), therefore exploration of A and B genomes was inevitable as they have been reported to be potential reservoirs of gene(s) for resistance to black rot. To utilize these sources, interspecific hybrid and backcross progeny (B1) were generated between cauliflower “Pusa Sharad” and Ethiopian mustard “NPC-9” employing in vitro embryo rescue technique. Direct ovule culture method was better than siliqua culture under different temperature regime periods. Hybridity testing of F1 inter-specific plants was carried out using co-dominant SSR marker and Brassica B and C genome-specific (DB and DC) primers. Meiosis in the di-genomic (BCC) interspecific hybrid of B. oleracea botrytis group (2n = 18, CC) × B. carinata (2n = 4x = 34, BBCC) was higly disorganized and cytological analysis of pollen mother cells revealed chromosomes 2n = 26 at metaphase-I. Fertile giant pollen grain formation was observed frequently in interspecific F1 hybrid and BC1 plants. The F1 inter-specific plants were found to be resistant to Xcc race 1. Segregation distortion was observed in BC1 generation for black rot resistance and different morphological traits. The At1g70610 marker analysis confirmed successful introgression of black rot resistance in interspecific BC1 population. This effort will go a long way in pyramiding gene(s) for resistance against black rot in Cole crops, especially cauliflower and cabbage for developing durable resistance, thus minimize dependency on bactericides. PMID:28769959

Introgression of Black Rot Resistance from Brassica carinata to Cauliflower (Brassica oleracea botrytis Group) through Embryo Rescue.

PubMed

Sharma, Brij B; Kalia, Pritam; Singh, Dinesh; Sharma, Tilak R

2017-01-01

Black rot caused by Xanthomonas campestris pv. campestris ( Xcc ) is a very important disease of cauliflower ( Brassica oleracea botrytis group) resulting into 10-50% yield losses every year. Since there is a dearth of availability of resistance to black rot disease in B. oleracea (C genome), therefore exploration of A and B genomes was inevitable as they have been reported to be potential reservoirs of gene(s) for resistance to black rot. To utilize these sources, interspecific hybrid and backcross progeny (B 1 ) were generated between cauliflower "Pusa Sharad" and Ethiopian mustard "NPC-9" employing in vitro embryo rescue technique. Direct ovule culture method was better than siliqua culture under different temperature regime periods. Hybridity testing of F 1 inter-specific plants was carried out using co-dominant SSR marker and Brassica B and C genome-specific (DB and DC) primers. Meiosis in the di-genomic (BCC) interspecific hybrid of B. oleracea botrytis group (2 n = 18, CC) × B. carinata (2 n = 4x = 34, BBCC) was higly disorganized and cytological analysis of pollen mother cells revealed chromosomes 2 n = 26 at metaphase-I. Fertile giant pollen grain formation was observed frequently in interspecific F 1 hybrid and BC 1 plants. The F 1 inter-specific plants were found to be resistant to Xcc race 1. Segregation distortion was observed in BC 1 generation for black rot resistance and different morphological traits. The At1g70610 marker analysis confirmed successful introgression of black rot resistance in interspecific BC 1 population. This effort will go a long way in pyramiding gene(s) for resistance against black rot in Cole crops, especially cauliflower and cabbage for developing durable resistance, thus minimize dependency on bactericides.

Comparison of transcriptome profiles by Fusarium oxysporum inoculation between Fusarium yellows resistant and susceptible lines in Brassica rapa L.

PubMed

Miyaji, Naomi; Shimizu, Motoki; Miyazaki, Junji; Osabe, Kenji; Sato, Maho; Ebe, Yusuke; Takada, Satoko; Kaji, Makoto; Dennis, Elizabeth S; Fujimoto, Ryo; Okazaki, Keiichi

2017-12-01

Resistant and susceptible lines in Brassica rapa have different immune responses against Fusarium oxysporum inoculation. Fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans (Foc) is an important disease of Brassicaceae; however, the mechanism of how host plants respond to Foc is still unknown. By comparing with and without Foc inoculation in both resistant and susceptible lines of Chinese cabbage (Brassica rapa var. pekinensis), we identified differentially expressed genes (DEGs) between the bulked inoculated (6, 12, 24, and 72 h after inoculation (HAI)) and non-inoculated samples. Most of the DEGs were up-regulated by Foc inoculation. Quantitative real-time RT-PCR showed that most up-regulated genes increased their expression levels from 24 HAI. An independent transcriptome analysis at 24 and 72 HAI was performed in resistant and susceptible lines. GO analysis using up-regulated genes at 24 HAI indicated that Foc inoculation activated systemic acquired resistance (SAR) in resistant lines and tryptophan biosynthetic process and responses to chitin and ethylene in susceptible lines. By contrast, GO analysis using up-regulated genes at 72 HAI showed the overrepresentation of some categories for the defense response in susceptible lines but not in the resistant lines. We also compared DEGs between B. rapa and Arabidopsis thaliana after F. oxysporum inoculation at the same time point, and identified genes related to defense response that were up-regulated in the resistant lines of Chinese cabbage and A. thaliana. Particular genes that changed expression levels overlapped between the two species, suggesting that they are candidates for genes involved in the resistance mechanisms against F. oxysporum.

Distribution of selenoglucosinolates and their metabolites in Brassica treated with sodium selenate.

PubMed

Matich, Adam J; McKenzie, Marian J; Lill, Ross E; McGhie, Tony K; Chen, Ronan K-Y; Rowan, Daryl D

2015-02-25

In Brassica species, hydrolysis of (methylthio)glucosinolates produces sulfur-containing aglycons which have demonstrated anticancer benefits. Selenized Brassicaceae contain (methylseleno)glucosinolates and their selenium-containing aglycons. As a prelude to biological testing, broccoli, cauliflower, and forage rape plants were treated with sodium selenate and their tap roots, stems, leaves, and florets analyzed for selenoglucosinolates and their Se aglycons. Two new selenoglucosinolates were identified: glucoselenoraphanin in broccoli florets and glucoselenonasturtiin in forage rape roots. A new aglycon, selenoberteroin nitrile, was identified in forage rape. The major selenoglucosinolates were glucoselenoerucin in broccoli, glucoselenoiberverin in cauliflower, and glucoselenoerucin and glucoselenoberteroin in forage rape roots. In broccoli florets, the concentrations of selenglucosinolates exceeded those of their sulfur analogues. Fertilization with selenium slightly reduced (methylthio)glucosinolates and aglycons in the roots, but increased them in the florets, the leaves, and sometimes the stems. These discoveries provide a new avenue for investigating how consumption of Brassica vegetables and their organoselenides may promote human health.

Molasses melanoidin-like products enhance phytoextraction of lead through three Brassica species.

PubMed

Hatano, Ken-Ichi; Yamatsu, Takeshi

2018-05-12

Previously, it has been suggested that melanoidin-like products (MLP) from sugarcane molasses may accelerate copper phytoextraction. In this study, we evaluated the facilitatory effect of MLP on phytoextraction in a medium including cadmium or lead, the concentrations of which were adjusted around the regulation values of the Soil Contamination Countermeasures Act in Japan. Three Brassica species were tested based on their fast growth, high biomass productivity, and high heavy metal absorption. Both biomass and lead uptake in the nutrient medium with 1 mM lead nitrate were significantly increased by the addition of MLP, and almost all of the lead was accumulated in the root tissue. Therefore, MLP were able both to detoxify lead ions and to improve their bioavailability in Brassica species. In contrast, only these species with MLP or citric acid survived in the nutrient medium with 1 mM cadmium sulfate. The phytoextraction of cadmium using these species was therefore impractical under the Act.

DNA-based identification of Brassica vegetable species for the juice industry.

PubMed

Etoh, Kazumi; Niijima, Noritaka; Yokoshita, Masahiko; Fukuoka, Shin-Ichi

2003-10-01

Since kale (Brassica oleracea var. acephala), a cruciferous vegetable with a high level of vitamins and functional compounds beneficial to health and wellness, has become widely used in the juice industry, a precise method for quality control of vegetable species is necessary. We describe here a DNA-based identification method to distinguish kale from cabbage (Brassica oleracea var. capitata), a closely related species, which can be inadvertently mixed with kale during the manufacturing process. Using genomic DNA from these vegetables and combinatory sets of nucleotide primers, we screened for random amplified polymorphic DNA (RAPD) fragments and found three cabbage-specific fragments. These RAPD fragments, with lengths of 1.4, 0.5, and 1.5 kb, were purified, subcloned, and sequenced. Based on sequence-tagged sites (STS), we designed sets of primers to detect cabbage-specific identification (CAI) DNA markers. Utilizing the CAI markers, we successfully distinguished more than 10 different local cabbage accessions from 20 kale accessions, and identified kale juices experimentally spiked with different amounts of cabbage.

Mercury-induced oxidative stress in Indian mustard (Brassica juncea L.).

PubMed

Shiyab, Safwan; Chen, Jian; Han, Fengxiang X; Monts, David L; Matta, Fank B; Gu, Mengmeng; Su, Yi; Masad, Motasim A

2009-10-01

Mercury, a potent neurotoxin, is released to the environment in significant amounts by both natural processes and anthropogenic activities. No natural hyperaccumulator plant has been reported for mercury phytoremediation. Few studies have been conducted on the physiological responses of Indian mustard, a higher biomass plant with faster growth rates, to mercury pollution. This study investigated the phytotoxicity of mercury to Indian mustard (Brassica juncea L.) and mercury-induced oxidative stress in order to examine the potential application of Indian mustard to mercury phytoremediation. Two common cultivars (Florida Broadleaf and Longstanding) of Indian mustard were grown hydroponically in a mercury-spiked solution. Plant uptake, antioxidative enzymes, peroxides, and lipid peroxidation under mercury stress were investigated. Antioxidant enzymes (catalase, CAT; peroxidase, POD; and superoxide dismutase, SOD) were the most sensitive indices of mercury-induced oxidative response of Indian mustard plants. Indian mustard effectively generated an enzymatic antioxidant defense system (especially CAT) to scavenge H(2)O(2), resulting in lower H(2)O(2) in shoots with higher mercury concentrations. These two cultivars of Indian mustard demonstrated an efficient metabolic defense and adaptation system to mercury-induced oxidative stress. A majority of Hg was accumulated in the roots and low translocations of Hg from roots to shoots were found in two cultivars of Indian mustard. Thus Indian mustard might be a potential candidate plant for phytofiltration/phytostabilization of mercury contaminated waters and wastewater.

Blood feeding of Ornithodoros turicata larvae using an artificial membrane system

USDA-ARS?s Scientific Manuscript database

An artificial membrane system was adapted to feed Ornithodoros turicata larvae from a laboratory colony using defibrinated swine blood. Aspects related to larval feeding and molting to the 1st nymphal instar were evaluated. Fifty-five percent of all larvae exposed to the artificial membrane in two e...

Differentiation of bacterial feeding nematodes in soil ecological studies by means of arbitrarily primed PCR

USGS Publications Warehouse

Van Der Knaap, Esther; Rodriguez, Russell J.; Freckman, Diana W.

1993-01-01

Arbitrarily-primed polymerase chain reaction (ap-PCR) was used to differentiate closely related bacterial-feeding nematodes of the genera: Caenorhabditis, Acrobeloides, Cephalobus and Zeldia. Average percentage similarity of bands generated by ap-PCR with seven different primers between 14 isolates of Caenorhabditis elegans was ⪢ 90%, whereas between C. elegans, C. briggsae and C. remanei similarity was < 20%. Based on intra- and inter-specific similarity between Caenorhabditis isolates, analysis of Acrobeloides, Cephalobus and Zeldia isolates revealed either similar or different genotypes. Distinct genotypes were verified by morphological analyses. In addition, the genotypes obtained from single egg-derived nematode populations were also obtained from ap-PCR analysis of single worms. Due to the difficulty of identification of soil nematodes, the ap-PCR offers potential as a rapid and reliable technique to assess biodiversity. Ap-PCR will make it feasible, for the first time, to study the ecological interactions of unique nematode genotypes in soil habitats.

Differentiation and adaptive radiation of amphibious gobies (Gobiidae: Oxudercinae) in semi-terrestrial habitats.

PubMed

Polgar, G; Sacchetti, A; Galli, P

2010-11-01

During several surveys made in the region of the lower Fly River and delta, Papua New Guinea, nine species of oxudercine gobies (Gobiidae: Oxudercinae) were recorded: Boleophthalmus caeruleomaculatus, Oxuderces wirzi, Periophthalmodon freycineti, Periophthalmus darwini, Periophthalmus novaeguineaensis, Periophthalmus takita, Periophthalmus weberi, Scartelaos histophorus and Zappa confluentus. An exploratory multivariate analysis of their habitat conditions discriminated five guilds, differentially distributed in habitats with different quantities of environmental water and three guilds corresponding to different levels of salinity. A partial correspondence between phylogenetic and ecological categories suggested the presence of parallel adaptive radiations within different genera. In particular, the species found in the most terrestrial habitats (P. weberi) was also found in the widest range of conditions, suggesting that colonization of extreme semi-terrestrial and freshwater habitats by this species was facilitated by eurytypy. It is proposed that these findings provide insight into convergent adaptations for the vertebrate eco-evolutionary transition from sea to land. © 2010 The Authors. Journal of Fish Biology © 2010 The Fisheries Society of the British Isles.

Responsive Feeding: Implications for Policy and Program Implementation12

PubMed Central

Engle, Patrice L.; Pelto, Gretel H.

2011-01-01

In this article, we examine responsive feeding as a nutrition intervention, with an emphasis on the development and incorporation of responsive feeding into policies and programs over the last 2 decades and recommendations for increasing the effectiveness of responsive feeding interventions. A review of policy documents from international agencies and high-income countries reveals that responsive feeding has been incorporated into nutrition policies. Official guidelines from international agencies, nongovernmental organizations, and professional organizations often include best practice recommendations for responsive feeding. Four potential explanations are offered for the rapid development of policies related to responsive feeding that have occurred despite the relatively recent recognition that responsive feeding plays a critical role in child nutrition and growth and the paucity of effectiveness trials to determine strategies to promote responsive feeding. Looking to the future, 3 issues related to program implementation are highlighted: 1) improving intervention specificity relative to responsive feeding; 2) developing protocols that facilitate efficient adaptation of generic guidelines to national contexts and local conditions; and 3) development of program support materials, including training, monitoring, and operational evaluation. PMID:21270361

Implementation of parental feeding practices: does parenting style matter?

PubMed

Kiefner-Burmeister, Allison; Hoffmann, Debra; Zbur, Samantha; Musher-Eizenman, Dara

2016-09-01

To combat childhood obesity, researchers have focused on parental feeding practices that promote child health. The current study investigated how parenting style relates to twelve parental feeding practices. Data on parenting style and parental feeding practices were obtained for a correlational study from users of Amazon's Mechanical Turk, an online survey system. USA. Mothers of children aged 7-11 years (n 193). Parenting style related differentially to eleven out of the twelve measured practices. Authoritative mothers displayed more feeding practices that promote child health and fewer practices that impede child health. Authoritarian and permissive mothers displayed more unhealthy practices than authoritative mothers, but differed from each other on the practices they employed. Parenting style may relate to more aspects of feeding than previously realized. The inclusion of numerous healthy feeding practices along with unhealthy practices in the current study provides suggestions for the application of healthy feeding behaviours. Instruction on feeding behaviours and parenting style should be a focus of future educational programmes.

Influence of chick hatch time and access to feed on broiler muscle development.

PubMed

Powell, D J; Velleman, S G; Cowieson, A J; Singh, M; Muir, W I

2016-06-01

The effect of hatch time and the timing of access to feed on growth rate and breast muscle development was assessed in Ross 308 broiler chickens. Chicks were removed from the incubator upon hatching, and classified as early (EH), midterm (MH), or late (LH) hatchers, based on the duration of their incubation. Feed and water were available either immediately at hatch, or 24 h after the conclusion of the hatch period. Hatchling body weight was uniform regardless of hatch time. Subsequently, bodyweight was increased in EH compared to LH birds following immediate access to feed, until 7 d in female, and 14 d in male birds. Relative breast weight was increased until 28 d in birds with immediate access to feed, and also EH and MH birds regardless of access to feed. Pectoralis major muscle morphology and expression of the myogenic regulatory factors myogenic determination factor 1 (MYOD1) and myogenin, and the proteoglycans syndecan-4, glypican-1, and decorin were measured. Myogenin and glypican-1 stimulate satellite cell (SC) differentiation. Glypican-1 expression was unaffected by treatment. A late increase in myogenin expression was observed in MH birds with delayed access to feed, and all LH birds. Syndecan-4 and MYOD1, expressed in proliferating SC, and decorin, which stimulates satellite cell proliferation and differentiation, were variably upregulated in the first wk posthatch in the same birds. These data suggest SC were activated and proliferating, but had reduced differentiation in later hatching and feed deprived birds. Conversely, EH birds with immediate access to feed had maximal myofiber width at 7 d, while fiber width was increased in birds with immediate access to feed compared to those with delayed access to feed through 40 d of age. These results demonstrate that delaying chick access to feed for 24 h upon removal from the incubator will impair muscle growth. Additionally, hatch time influences muscle development, with accelerated muscle growth in EH and

Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L

USDA-ARS?s Scientific Manuscript database

The crop species Brassica rapa L. has significant economic importance around the globe. Crop domestication and improvement has resulted in extreme phenotypic diversity and subspecies that are used for oilseed, food for human consumption and fodder for livestock. However, the global distribution and ...

Bioinformatics analysis of the phytoene synthase gene in cabbage (Brassica oleracea var. capitata)

NASA Astrophysics Data System (ADS)

Sun, Bo; Jiang, Min; Xue, Shengling; Zheng, Aihong; Zhang, Fen; Tang, Haoru

2018-04-01

Phytoene Synthase (PSY) is an important enzyme in carotenoid biosynthesis. Here, the Brassica oleracea var. capitata PSY (BocPSY) gene sequences were obtained from Brassica database (BRAD), and preformed for bioinformatics analysis. The BocPSY1, BocPSY2 and BocPSY3 genes mapped to chromosomes 2,3 and 9, and contains an open reading frame of 1,248 bp, 1,266 bp and 1,275 bp that encodes a 415, 421, 424 amino acid protein, respectively. Subcellular localization predicted all BocPSY genes were in the chloroplast. The conserved domain of the BocPSY protein is PLN02632. Homology analysis indicates that the levels of identity among BocPSYs were all more than 85%, and the PSY protein is apparently conserved during plant evolution. The findings of the present study provide a molecular basis for the elucidation of PSY gene function in cabbage.

Adaptive Myogenesis under Hypoxia

PubMed Central

Yun, Zhong; Lin, Qun; Giaccia, Amato J.

2005-01-01

Previous studies have indicated that myoblasts can differentiate and repair muscle injury after an ischemic insult. However, it is unclear how hypoxia or glucose deprivation in the ischemic microenvironment affects myoblast differentiation. We have found that myogenesis can adapt to hypoxic conditions. This adaptive mechanism is accompanied by initial inhibition of the myoD, E2A, and myogenin genes followed by resumption of their expression in an oxygen-dependent manner. The regulation of myoD transcription by hypoxia is correlated with transient deacetylation of histones associated with the myoD promoter. It is noteworthy that, unlike the differentiation of other cell types such as preadipocytes or chondroblasts, the effect of hypoxia on myogenesis is independent of HIF-1, a ubiquitous regulator of transcription under hypoxia. While myogenesis can also adapt to glucose deprivation, the combination of severe hypoxia and glucose deprivation found in an ischemic environment results in pronounced loss of myoblasts. Our studies indicate that the ischemic muscle can be repaired via the adaptive differentiation of myogenic precursors, which depends on the levels of oxygen and glucose in the ischemic microenvironment. PMID:15798192

Flowering times in genetically modified Brassica hybrids in the absence of selection

EPA Science Inventory

Changes in days to flowering (DTF) were observed among reciprocal F1 progeny of Brassica napus ‘RaideRR’ with other B. napus and also with weedy B. rapa. Changes in DTF are presented as factors to consider in evaluating the potential of crop to weed gene flow in different geograp...

Independent AMP and NAD signaling regulates C2C12 differentiation and metabolic adaptation.

PubMed

Hsu, Chia George; Burkholder, Thomas J

2016-12-01

The balance of ATP production and consumption is reflected in adenosine monophosphate (AMP) and nicotinamide adenine dinucleotide (NAD) content and has been associated with phenotypic plasticity in striated muscle. Some studies have suggested that AMPK-dependent plasticity may be an indirect consequence of increased NAD synthesis and SIRT1 activity. The primary goal of this study was to assess the interaction of AMP- and NAD-dependent signaling in adaptation of C2C12 myotubes. Changes in myotube developmental and metabolic gene expression were compared following incubation with 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) and nicotinamide mononucleotide (NMN) to activate AMPK- and NAD-related signaling. AICAR showed no effect on NAD pool or nampt expression but significantly reduced histone H3 acetylation and GLUT1, cytochrome C oxidase subunit 2 (COX2), and MYH3 expression. In contrast, NMN supplementation for 24 h increased NAD pool by 45 % but did not reduce histone H3 acetylation nor promote mitochondrial gene expression. The combination of AMP and NAD signaling did not induce further metabolic adaptation, but NMN ameliorated AICAR-induced myotube reduction. We interpret these results as indication that AMP and NAD contribute to C2C12 differentiation and metabolic adaptation independently.

Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops.

PubMed

Vicente, Joana G; Holub, Eric B

2013-01-01

Xanthomonas campestris pv. campestris (Xcc) (Pammel) Dowson is a Gram-negative bacterium that causes black rot, the most important disease of vegetable brassica crops worldwide. Intensive molecular investigation of Xcc is gaining momentum and several whole genome sequences are available. Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadacea; Genus Xanthomonas; Species X. campestris. Xcc can cause disease in a large number of species of Brassicaceae (ex-Cruciferae), including economically important vegetable Brassica crops and a number of other cruciferous crops, ornamentals and weeds, including the model plant Arabidopsis thaliana. Black rot is a systemic vascular disease. Typical disease symptoms include V-shaped yellow lesions starting from the leaf margins and blackening of the veins. Collections of Xcc isolates have been differentiated into physiological races based on the response of several brassica species lines. Black rot is a seed-borne disease. The disease is favoured by warm, humid conditions and can spread rapidly from rain dispersal and irrigation water. The control of black rot is difficult and relies on the use of pathogen-free planting material and the elimination of other potential inoculum sources (infected crop debris and cruciferous weeds). Major gene resistance is very rare in B. oleracea (brassica C genome). Resistance is more readily available in other species, including potentially useful sources of broad-spectrum resistance in B. rapa and B. carinata (A and BC genomes, respectively) and in the wild relative A. thaliana. The reference genomes of three isolates have been released. The genome consists of a single chromosome of approximately 5 100 000 bp, with a GC content of approximately 65% and an average predicted number of coding DNA sequences (CDS) of 4308. Three different secretion systems have been identified and studied in Xcc. The gene clusters xps and xcs encode a type II

New evidence for mammaliaform ear evolution and feeding adaptation in a Jurassic ecosystem

NASA Astrophysics Data System (ADS)

Luo, Zhe-Xi; Meng, Qing-Jin; Grossnickle, David M.; Liu, Di; Neander, April I.; Zhang, Yu-Guang; Ji, Qiang

2017-08-01

Stem mammaliaforms are forerunners to modern mammals, and they achieved considerable ecomorphological diversity in their own right. Recent discoveries suggest that eleutherodontids, a subclade of Haramiyida, were more species-rich during the Jurassic period in Asia than previously recognized. Here we report a new Jurassic eleutherodontid mammaliaform with an unusual mosaic of highly specialized characteristics, and the results of phylogenetic analyses that support the hypothesis that haramiyidans are stem mammaliaforms. The new fossil shows fossilized skin membranes that are interpreted to be for gliding and a mandibular middle ear with a unique character combination previously unknown in mammaliaforms. Incisor replacement is prolonged until well after molars are fully erupted, a timing pattern unique to most other mammaliaforms. In situ molar occlusion and a functional analysis reveal a new mode of dental occlusion: dual mortar-pestle occlusion of opposing upper and lower molars, probably for dual crushing and grinding. This suggests that eleutherodontids are herbivorous, and probably specialized for granivory or feeding on soft plant tissues. The inferred dietary adaptation of eleutherodontid gliders represents a remarkable evolutionary convergence with herbivorous gliders in Theria. These Jurassic fossils represent volant, herbivorous stem mammaliaforms associated with pre-angiosperm plants that appear long before the later, iterative associations between angiosperm plants and volant herbivores in various therian clades.

New evidence for mammaliaform ear evolution and feeding adaptation in a Jurassic ecosystem.

PubMed

Luo, Zhe-Xi; Meng, Qing-Jin; Grossnickle, David M; Liu, Di; Neander, April I; Zhang, Yu-Guang; Ji, Qiang

2017-08-17

Stem mammaliaforms are forerunners to modern mammals, and they achieved considerable ecomorphological diversity in their own right. Recent discoveries suggest that eleutherodontids, a subclade of Haramiyida, were more species-rich during the Jurassic period in Asia than previously recognized. Here we report a new Jurassic eleutherodontid mammaliaform with an unusual mosaic of highly specialized characteristics, and the results of phylogenetic analyses that support the hypothesis that haramiyidans are stem mammaliaforms. The new fossil shows fossilized skin membranes that are interpreted to be for gliding and a mandibular middle ear with a unique character combination previously unknown in mammaliaforms. Incisor replacement is prolonged until well after molars are fully erupted, a timing pattern unique to most other mammaliaforms. In situ molar occlusion and a functional analysis reveal a new mode of dental occlusion: dual mortar-pestle occlusion of opposing upper and lower molars, probably for dual crushing and grinding. This suggests that eleutherodontids are herbivorous, and probably specialized for granivory or feeding on soft plant tissues. The inferred dietary adaptation of eleutherodontid gliders represents a remarkable evolutionary convergence with herbivorous gliders in Theria. These Jurassic fossils represent volant, herbivorous stem mammaliaforms associated with pre-angiosperm plants that appear long before the later, iterative associations between angiosperm plants and volant herbivores in various therian clades.

Biotechnological applications in in vitro plant regeneration studies of broccoli (Brassica oleracea L. var. italica), an important vegetable crop.

PubMed

Kumar, Pankaj; Srivastava, Dinesh Kumar

2016-04-01

Biotechnology holds promise for genetic improvement of important vegetable crops. Broccoli (Brassica oleracea L. var. italica) is an important vegetable crop of the family Brassicaceae. However, various biotic and abiotic stresses cause enormous crop yield losses during commercial cultivation of broccoli. Establishment of a reliable, reproducible and efficient in vitro plant regeneration system with cell and tissue culture is a vital prerequisite for biotechnological application of crop improvement programme. An in vitro plant regeneration technique refers to culturing, cell division, cell multiplication, de-differentiation and differentiation of cells, protoplasts, tissues and organs on defined liquid/solid medium under aseptic and controlled environment. Recent progress in the field of plant tissue culture has made this area one of the most dynamic and promising in experimental biology. There are many published reports on in vitro plant regeneration studies in broccoli including direct organogenesis, indirect organogenesis and somatic embryogenesis. This review summarizes those plant regeneration studies in broccoli that could be helpful in drawing the attention of the researchers and scientists to work on it to produce healthy, biotic and abiotic stress resistant plant material and to carry out genetic transformation studies for the production of transgenic plants.

The effect of pre-enrichment media on the recovery and detection of Salmonella in feed

USDA-ARS?s Scientific Manuscript database

Current methodology for detecting Salmonella in feeds and feed ingredients are adapted from food safety methods. These methods do not take into account the stressed state of Salmonella in feed, presence of competing microorganisms nor the sample matrix. The objective was to evaluate four pre-enrichm...

Carotenoids, polyphenols and micronutrient profiles of Brassica oleraceae and plum varieties and their contribution to measures of total antioxidant capacity.

PubMed

Kaulmann, Anouk; Jonville, Marie-Caroline; Schneider, Yves-Jacques; Hoffmann, Lucien; Bohn, Torsten

2014-07-15

The consumption of phytochemicals such as carotenoids and polyphenols within whole fruits and vegetables has been associated with decreased incidence of various inflammation and oxidative stress related chronic diseases, which may be due to direct antioxidant effects, or indirect mechanisms such as affecting signal transduction/gene expression. Within the present study, we investigated the antioxidant composition of two major groups of vegetables and fruits, Brassica oleraceae and prunus spp., and estimated their contribution to antioxidant capacity. For this purpose, 17 plum and 27 Brassica varieties were collected in Luxembourg, and analysed for their individual polyphenol and carotenoid profile, vitamin C, dietary fibre, and minerals/trace elements, and their correlation with markers of antioxidant capacity (FRAP, ABTS, Folin-Ciocalteu). Total carotenoid and polyphenol content varied considerably between the different Brassica and plum varieties, with highest concentrations in the variety Kale (13.3 ± 0.58 mg/100g wet weight) and Cherry plum (1.96 ± 0.28 mg/100g) for carotenoids; and Kale (27.0 ± 0.91 mg/100g) and Kirks plum (185 ± 14 mg/100g) for polyphenols. In developed multiple linear-regression-models for Brassica, flavonoids, anthocyanins, lutein and vitamin C were found to be the best predictors of antioxidant capacity as assessed by FRAP (R(2)=0.832) and flavonoids, neochlorogenic acid and vitamin C as assessed by ABTS (R(2)=0.831); while for plums these were selenium, total sugars, chlorogenic acid and vitamin C (R(2)=0.853), and selenium, chlorogenic acid and flavonoids for FRAP (R(2)=0.711). When considering Brassica and plum consumption in Luxembourg, it is estimated that both contribute to an antioxidant intake equivalent to 26 and 6 mg per day of ascorbic acid equivalents, respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

The reference transcriptome of the adult female biting midge (Culicoides sonorensis) and differential gene expression profiling during teneral, blood, and sucrose feeding conditions.

PubMed

Nayduch, Dana; Lee, Matthew B; Saski, Christopher A

2014-01-01

Unlike other important vectors such as mosquitoes and sandflies, genetic and genomic tools for Culicoides biting midges are lacking, despite the fact that they vector a large number of arboviruses and other pathogens impacting humans and domestic animals world-wide. In North America, female Culicoides sonorensis midges are important vectors of bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV), orbiviruses that cause significant disease in livestock and wildlife. Libraries of tissue-specific transcripts expressed in response to feeding and oral orbivirus challenge in C. sonorensis have previously been reported, but extensive genome-wide expression profiling in the midge has not. Here, we successfully used deep sequencing technologies to construct the first adult female C. sonorensis reference transcriptome, and utilized genome-wide expression profiling to elucidate the genetic response to blood and sucrose feeding over time. The adult female midge unigene consists of 19,041 genes, of which less than 7% are differentially expressed during the course of a sucrose meal, while up to 52% of the genes respond significantly in blood-fed midges, indicating hematophagy induces complex physiological processes. Many genes that were differentially expressed during blood feeding were associated with digestion (e.g. proteases, lipases), hematophagy (e.g., salivary proteins), and vitellogenesis, revealing many major metabolic and biological factors underlying these critical processes. Additionally, key genes in the vitellogenesis pathway were identified, which provides the first glimpse into the molecular basis of anautogeny for C. sonorensis. This is the first extensive transcriptome for this genus, which will serve as a framework for future expression studies, RNAi, and provide a rich dataset contributing to the ultimate goal of informing a reference genome assembly and annotation. Moreover, this study will serve as a foundation for subsequent studies of

Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication.

PubMed

Zhao, Meixia; Du, Jianchang; Lin, Feng; Tong, Chaobo; Yu, Jingyin; Huang, Shunmou; Wang, Xiaowu; Liu, Shengyi; Ma, Jianxin

2013-10-01

Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution. © 2013 Purdue University The Plant Journal © 2013 John Wiley & Sons Ltd.

Comparative Analysis of Disease-Linked Single Nucleotide Polymorphic Markers from Brassica rapa for Their Applicability to Brassica oleracea

PubMed Central

Cho, Young-Il; Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Lee, Hye-Eun; Kim, Do-Sun

2015-01-01

Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH—developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP—based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS—derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species. PMID:25790283

Glucosinolates in Brassica vegetables: the influence of the food supply chain on intake, bioavailability and human health.

PubMed

Verkerk, Ruud; Schreiner, Monika; Krumbein, Angelika; Ciska, Ewa; Holst, Birgit; Rowland, Ian; De Schrijver, Remi; Hansen, Magnor; Gerhäuser, Clarissa; Mithen, Richard; Dekker, Matthijs

2009-09-01

Glucosinolates (GLSs) are found in Brassica vegetables. Examples of these sources include cabbage, Brussels sprouts, broccoli, cauliflower and various root vegetables (e.g. radish and turnip). A number of epidemiological studies have identified an inverse association between consumption of these vegetables and the risk of colon and rectal cancer. Animal studies have shown changes in enzyme activities and DNA damage resulting from consumption of Brassica vegetables or isothiocyanates, the breakdown products (BDP) of GLSs in the body. Mechanistic studies have begun to identify the ways in which the compounds may exert their protective action but the relevance of these studies to protective effects in the human alimentary tract is as yet unproven. In vitro studies with a number of specific isothiocyanates have suggested mechanisms that might be the basis of their chemoprotective effects. The concentration and composition of the GLSs in different plants, but also within a plant (e.g. in the seeds, roots or leaves), can vary greatly and also changes during plant development. Furthermore, the effects of various factors in the supply chain of Brassica vegetables including breeding, cultivation, storage and processing on intake and bioavailability of GLSs are extensively discussed in this paper.

Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards.

PubMed

Akashi, Hiroshi D; Cádiz Díaz, Antonio; Shigenobu, Shuji; Makino, Takashi; Kawata, Masakado

2016-05-01

How animals achieve evolutionary adaptation to different thermal environments is an important issue for evolutionary biology as well as for biodiversity conservation in the context of recent global warming. In Cuba, three sympatric species of Anolis lizards (Anolis allogus, A. homolechis and A. sagrei) inhabit different thermal microhabitats, thereby providing an excellent opportunity to examine how they have adapted to different environmental temperatures. Here, we performed RNA-seq on the brain, liver and skin tissues from these three species to analyse their transcriptional responses at two different temperatures. In total, we identified 400, 816 and 781 differentially expressed genes (DEGs) between the two temperatures in A. allogus, A. homolechis and A. sagrei, respectively. Only 62 of these DEGs were shared across the three species, indicating that global transcriptional responses have diverged among these species. Gene ontology (GO) analysis showed that large numbers of ribosomal protein genes were DEGs in the warm-adapted A. homolechis, suggesting that the upregulation of protein synthesis is an important physiological mechanism in the adaptation of this species to hotter environments. GO analysis also showed that GO terms associated with circadian regulation were enriched in all three species. A gene associated with circadian regulation, Nr1d1, was detected as a DEG with opposite expression patterns between the cool-adapted A. allogus and the hot-adapted A. sagrei. Because the environmental temperature fluctuates more widely in open habitats than in forests throughout the day, the circadian thermoregulation could also be important for adaptation to distinct thermal habitats. © 2016 John Wiley & Sons Ltd.

Plastid transformation in cabbage (Brassica oleracea L. var. capitata L.) by the biolistic process.

PubMed

Tseng, Menq-Jiau; Yang, Ming-Te; Chu, Wan-Ru; Liu, Cheng-Wei

2014-01-01

Cabbage (Brassica oleracea L. var. capitata L.) is one of the most important vegetable crops grown worldwide. Scientists are using biotechnology in addition to traditional breeding methods to develop new cabbage varieties with desirable traits. Recent biotechnological advances in chloroplast transformation technology have opened new avenues for crop improvement. In 2007, we developed a stable plastid transformation system for cabbage and reported the successful transformation of the cry1Ab gene into the cabbage chloroplast genome. This chapter describes the methods for cabbage transformation using biolistic procedures. The following sections are included in this protocol: preparation of donor materials, coating gold particles with DNA, biolistic bombardment, as well as the regeneration and selection of transplastomic cabbage plants. The establishment of a plastid transformation system for cabbage offers new possibilities for introducing new agronomic and horticultural traits into Brassica crops.

Concentrations of thiocyanate and goitrin in human plasma, their precursor concentrations in brassica vegetables, and associated potential risk for hypothyroidism.

PubMed

Felker, Peter; Bunch, Ronald; Leung, Angela M

2016-04-01

Brassica vegetables are common components of the diet and have beneficial as well as potentially adverse health effects. Following enzymatic breakdown, some glucosinolates in brassica vegetables produce sulforaphane, phenethyl, and indolylic isothiocyanates that possess anticarcinogenic activity. In contrast, progoitrin and indolylic glucosinolates degrade to goitrin and thiocyanate, respectively, and may decrease thyroid hormone production. Radioiodine uptake to the thyroid is inhibited by 194 μmol of goitrin, but not by 77 μmol of goitrin. Collards, Brussels sprouts, and some Russian kale (Brassica napus) contain sufficient goitrin to potentially decrease iodine uptake by the thyroid. However, turnip tops, commercial broccoli, broccoli rabe, and kale belonging to Brassica oleracae contain less than 10 μmol of goitrin per 100-g serving and can be considered of minimal risk. Using sulforaphane plasma levels following glucoraphanin ingestion as a surrogate for thiocyanate plasma concentrations after indole glucosinolate ingestion, the maximum thiocyanate contribution from indole glucosinolate degradation is estimated to be 10 μM, which is significantly lower than background plasma thiocyanate concentrations (40-69 μM). Thiocyanate generated from consumption of indole glucosinolate can be assumed to have minimal adverse risks for thyroid health. © The Author(s) 2016. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Persistence and Dissipation of Chlorpyrifos in Brassica Chinensis, Lettuce, Celery, Asparagus Lettuce, Eggplant, and Pepper in a Greenhouse

PubMed Central

Lu, Meng-Xiao; Jiang, Wayne W.; Wang, Jia-Lei; Jian, Qiu; Shen, Yan; Liu, Xian-Jin; Yu, Xiang-Yang

2014-01-01

The residue behavior of chlorpyrifos, which is one of the extensively used insecticides all around the world, in six vegetable crops was assessed under greenhouse conditions. Each of the vegetables was subjected to a foliar treatment with chlorpyrifos. Two analytical methods were developed using gas chromatography equipped with a micro-ECD detector (LOQ = 0.05 mg kg−1) and liquid chromatography with a tandem mass spectrometry (LOQ = 0.01 mg kg−1). The initial foliar deposited concentration of chlorpyrifos (mg kg−1) on the six vegetables followed the increasing order of brassica chinensisbrassica chinensis) to 74.0±5.9 mg kg−1 (pepper plant). At pre-harvest interval 21 days, the chlorpyrifos residues in edible parts of the crops were <0.01 (eggplant fruit), <0.01 (pepper fruit), 0.56 (lettuce), 0.97 (brassica chinensis), 1.47 (asparagus lettuce), and 3.50 mg kg−1 (celery), respectively. The half-lives of chlorpyrifos were found to be 7.79 (soil), 2.64 (pepper plants), 3.90 (asparagus lettuce), 3.92 (lettuce), 5.81 (brassica chinensis), 3.00 (eggplant plant), and 5.45 days (celery), respectively. The dissipation of chlorpyrifos in soil and the six selected plants was different, indicating that the persistence of chlorpyrifos residues strongly depends upon leaf characteristics of the selected vegetables. PMID:24967589

Elucidating the interaction between light competition and herbivore feeding patterns using functional-structural plant modelling.

PubMed

de Vries, Jorad; Poelman, Erik H; Anten, Niels; Evers, Jochem B

2018-01-24

Plants usually compete with neighbouring plants for resources such as light as well as defend themselves against herbivorous insects. This requires investment of limiting resources, resulting in optimal resource distribution patterns and trade-offs between growth- and defence-related traits. A plant's competitive success is determined by the spatial distribution of its resources in the canopy. The spatial distribution of herbivory in the canopy in turn differs between herbivore species as the level of herbivore specialization determines their response to the distribution of resources and defences in the canopy. Here, we investigated to what extent competition for light affects plant susceptibility to herbivores with different feeding preferences. To quantify interactions between herbivory and competition, we developed and evaluated a 3-D spatially explicit functional-structural plant model for Brassica nigra that mechanistically simulates competition in a dynamic light environment, and also explicitly models leaf area removal by herbivores with different feeding preferences. With this novel approach, we can quantitatively explore the extent to which herbivore feeding location and light competition interact in their effect on plant performance. Our results indicate that there is indeed a strong interaction between levels of plant-plant competition and herbivore feeding preference. When plants did not compete, herbivory had relatively small effects irrespective of feeding preference. Conversely, when plants competed, herbivores with a preference for young leaves had a strong negative effect on the competitiveness and subsequent performance of the plant, whereas herbivores with a preference for old leaves did not. Our study predicts how plant susceptibility to herbivory depends on the composition of the herbivore community and the level of plant competition, and highlights the importance of considering the full range of dynamics in plant-plant-herbivore interactions

Elucidating the interaction between light competition and herbivore feeding patterns using functional–structural plant modelling

PubMed Central

de Vries, Jorad; Poelman, Erik H; Anten, Niels; Evers, Jochem B

2018-01-01

Abstract Background and Aims Plants usually compete with neighbouring plants for resources such as light as well as defend themselves against herbivorous insects. This requires investment of limiting resources, resulting in optimal resource distribution patterns and trade-offs between growth- and defence-related traits. A plant’s competitive success is determined by the spatial distribution of its resources in the canopy. The spatial distribution of herbivory in the canopy in turn differs between herbivore species as the level of herbivore specialization determines their response to the distribution of resources and defences in the canopy. Here, we investigated to what extent competition for light affects plant susceptibility to herbivores with different feeding preferences. Methods To quantify interactions between herbivory and competition, we developed and evaluated a 3-D spatially explicit functional–structural plant model for Brassica nigra that mechanistically simulates competition in a dynamic light environment, and also explicitly models leaf area removal by herbivores with different feeding preferences. With this novel approach, we can quantitatively explore the extent to which herbivore feeding location and light competition interact in their effect on plant performance. Key Results Our results indicate that there is indeed a strong interaction between levels of plant–plant competition and herbivore feeding preference. When plants did not compete, herbivory had relatively small effects irrespective of feeding preference. Conversely, when plants competed, herbivores with a preference for young leaves had a strong negative effect on the competitiveness and subsequent performance of the plant, whereas herbivores with a preference for old leaves did not. Conclusions Our study predicts how plant susceptibility to herbivory depends on the composition of the herbivore community and the level of plant competition, and highlights the importance of considering

Glucosinolates profile and antioxidant capacity of Romanian Brassica vegetables obtained by organic and conventional agricultural practices.

PubMed

Vicas, Simona I; Teusdea, Alin C; Carbunar, Mihai; Socaci, Sonia A; Socaciu, Carmen

2013-09-01

The profile of glucosinolates in relation to the antioxidant capacity of five Brassica vegetables (Broccoli, Cauliflower, Kohlrabi, White and Red Cabbage) grown by organic and conventional agricultural practices in Transylvania region-Romania, were determined and compared. The qualitative and quantitative compositions of glucosinolates were determined by HPLC-PDA technique. The antioxidant capacity was comparatively determined by ABTS, DPPH, FRAP and Folin-Ciocalteu assays. The highest glucosinolates levels were found in the Broccoli samples grown under conventional practices (14.24 μmol/g dry weight), glucoraphanin, glucobrassicin and neo-glucobrassicin being the major components. The total glucosinolates content was similar in Kohlrabi and Cauliflower (4.89 and 4.84 μmol/g dry weight, respectively), the indolyl glucosinolates were predominant in Kohlrabi, while the aliphatic derivatives (sinigrin and glucoiberin) were major in Cauliflower. In Cabbage samples, the aliphatic glucosinolates were predominat against indolyl derivatives, glucoraphanin and glucoiberin being the main ones in Red Cabbage. The principal component analysis was applied to discriminate among conventional and organic samples and demonstrated non-overlaps between these two agricultural practices. Meanwhile it was shown that glucosinolates may represent appropriate molecular markers of Brassica vegetables, their antioxidant capacity being higher in organic crops, without significant differences among different Brassica varieties.

Genetic Evidence of Human Adaptation to a Cooked Diet

PubMed Central

Carmody, Rachel N.; Dannemann, Michael; Briggs, Adrian W.; Nickel, Birgit; Groopman, Emily E.; Wrangham, Richard W.; Kelso, Janet

2016-01-01

Humans have been argued to be biologically adapted to a cooked diet, but this hypothesis has not been tested at the molecular level. Here, we combine controlled feeding experiments in mice with comparative primate genomics to show that consumption of a cooked diet influences gene expression and that affected genes bear signals of positive selection in the human lineage. Liver gene expression profiles in mice fed standardized diets of meat or tuber were affected by food type and cooking, but not by caloric intake or consumer energy balance. Genes affected by cooking were highly correlated with genes known to be differentially expressed in liver between humans and other primates, and more genes in this overlap set show signals of positive selection in humans than would be expected by chance. Sequence changes in the genes under selection appear before the split between modern humans and two archaic human groups, Neandertals and Denisovans, supporting the idea that human adaptation to a cooked diet had begun by at least 275,000 years ago. PMID:26979798

Stable isotope-labelled feed nutrients to assess nutrient-specific feed passage kinetics in ruminants.

PubMed

Warner, Daniel; Dijkstra, Jan; Hendriks, Wouter H; Pellikaan, Wilbert F

2014-03-30

Knowledge of digesta passage kinetics in ruminants is essential to predict nutrient supply to the animal in relation to optimal animal performance, environmental pollution and animal health. Fractional passage rates (FPR) of feed are widely used in modern feed evaluation systems and mechanistic rumen models, but data on nutrient-specific FPR are scarce. Such models generally rely on conventional external marker techniques, which do not always describe digesta passage kinetics in a satisfactory manner. Here the use of stable isotope-labelled dietary nutrients as a promising novel tool to assess nutrient-specific passage kinetics is discussed. Some major limitations of this technique include a potential marker migration, a poor isotope distribution in the labelled feed and a differential disappearance rate of isotopes upon microbial fermentation in non-steady state conditions. Such limitations can often be circumvented by using intrinsically stable isotope-labelled plant material. Data are limited but indicate that external particulate markers overestimate rumen FPR of plant fibre compared with the internal stable isotope markers. Stable isotopes undergo the same digestive mechanism as the labelled feed components and are thus of particular interest to specifically measure passage kinetics of digestible dietary nutrients. © 2013 Society of Chemical Industry.

Evaluation and Management of Neonatal Dysphagia: Impact of Pharyngoesophageal Motility Studies and Multidisciplinary Feeding Strategy

PubMed Central

Jadcherla, Sudarshan R.; Stoner, Erin; Gupta, Alankar; Bates, D. Gregory; Fernandez, Soledad; Di Lorenzo, Carlo; Linscheid, Thomas

2013-01-01

Background and objectives Abnormal swallowing (dysphagia) among neonates is commonly evaluated using the videofluoroscopic swallow study (VSS). Radiological findings considered high risk for administration of oral feeding include nasopharyngeal reflux, laryngeal penetration, aspiration, or pooling. Our aims were to determine pharyngoesophageal motility correlates in neonates with dysphagia and the impact of multidisciplinary feeding strategy. Methods Twenty dysphagic neonates (mean gestation ± standard deviation [SD] = 30.9 ± 4.9 weeks; median 31.1 weeks; range = 23.7–38.6 weeks) with abnormal VSS results were evaluated at 49.9 ± 16.5 weeks (median 41.36 weeks) postmenstrual age. The subjects underwent a swallow-integrated pharyngoesophageal motility assessment of basal and adaptive swallowing reflexes using a micromanometry catheter and pneumohydraulic water perfusion system. Based on observations during the motility study, multidisciplinary feeding strategies were applied and included postural adaptation, sensory modification, hunger manipulation, and operant conditioning methods. To discriminate pharyngoesophageal manometry correlates between oral feeders and tube feeders, data were stratified based on the primary feeding method at discharge, oral feeding versus tube feeding. Results At discharge, 15 of 20 dysphagic neonates achieved oral feeding success, and the rest required chronic tube feeding. Pharyngoesophageal manometry correlates were significantly different (P <0.05) between the primary oral feeders versus the chronic tube feeders for swallow frequency, swallow propagation, presence of adaptive peristaltic reflexes, oral feeding challenge test results, and upper esophageal sphincter tone. VSS results or disease characteristics had little effect on the feeding outcomes (P = NS). Conclusions Swallow-integrated esophageal motility studies permit prolonged evaluation of swallowing reflexes and responses to stimuli under controlled conditions at

Anaerobic soil disinfestation and Brassica seed meal amendment alter soil microbiology and system resistance

USDA-ARS?s Scientific Manuscript database

Brassica seed meal amendments and anaerobic soil disinfestation control a spectrum of soil-borne plant pathogens via a diversity of mechanisms. Transformations in microbial community structure and function in certain instances were determinants of disease control and enhanced plant performance. Fo...

Character of cellulase activity in the guts of flagellate-free termites with different feeding habits.

PubMed

Li, Zhi-Qiang; Liu, Bing-Rong; Zeng, Wen-Hui; Xiao, Wei-Liang; Li, Qiu-Jian; Zhong, Jun-Hong

2013-01-01

Cellulose digestion in termites (Isoptera) is highly important for ecological reasons and applications in biofuel conversion. The speciose Termitidae family has lost flagellates in the hindgut and developed diverse feeding habits. To address the response of cellulase activity to the differentiation of feeding habits, a comparative study of the activity and distribution of composite cellulases, endo-β-1,4-glucanase, and β-glucosidase was performed in seven common flagellate-free termites with three feeding habits: the humus-feeding termites Sinocapritermes mushae (Oshima et Maki), Malaysiocapritermes zhangfengensis Zhu, Yang et Huang and Pericapritermes jiangtsekiangensis (Kemner); the fungus-growing termites Macrotermes barneyi Light and Odontotermes formosanus (Shiraki); and the wood-feeding termites Nasutitermes parvonasutus (Shiraki) and Havilanditermes orthonasus (Tsai et Chen). The results showed that in diverse feeding groups, the wood-feeding group had the highest total composite cellulase and endo-β-1,4-glucanase activities, while the fungus-growing group had the highest β-glucosidase activity. In terms of the distribution of cellulase activity in the alimentary canals, the cellulase activities in wood-feeding termites were concentrated in the midgut, but there was no significant difference between all gut segments in humus-feeding termites. As for the fungus-growing termites, the main site of composite cellulase activity was in the midgut. The endo-β-1,4-glucanase activity was restricted to the midgut, but the primary site of β-glucosidase activity was in the foregut and the midgut (Mac. barneyi). The functions of the gut segments apparently differentiated between feeding groups. The results suggest that the differentiation of feeding habits in flagellate-free termites was characterized by the distribution of cellulases in the gut rather than by variations in cellulase activity.

Character of Cellulase Activity in the Guts of Flagellate-Free Termites with Different Feeding Habits

PubMed Central

Li, Zhi-Qiang; Liu, Bing-Rong; Zeng, Wen-Hui; Xiao, Wei-Liang; Li, Qiu-Jian; Zhong, Jun-Hong

2013-01-01

Cellulose digestion in termites (Isoptera) is highly important for ecological reasons and applications in biofuel conversion. The speciose Termitidae family has lost flagellates in the hindgut and developed diverse feeding habits. To address the response of cellulase activity to the differentiation of feeding habits, a comparative study of the activity and distribution of composite cellulases, endo-β-1, 4-glucanase, and β-glucosidase was performed in seven common flagellate-free termites with three feeding habits: the humus-feeding termites Sinocapritermes mushae (Oshima et Maki), Malaysiocapritermes zhangfengensis Zhu, Yang et Huang and Pericapritermes jiangtsekiangensis (Kemner); the fungus-growing termites Macrotermes barneyi Light and Odontotermes formosanus (Shiraki); and the wood-feeding termites Nasutitermes parvonasutus (Shiraki) and Havilanditermes orthonasus (Tsai et Chen). The results showed that in diverse feeding groups, the wood-feeding group had the highest total composite cellulase and endo-β-1, 4-glucanase activities, while the fungus-growing group had the highest β-glucosidase activity. In terms of the distribution of cellulase activity in the alimentary canals, the cellulase activities in wood-feeding termites were concentrated in the midgut, but there was no significant difference between all gut segments in humus-feeding termites. As for the fungus-growing termites, the main site of composite cellulase activity was in the midgut. The endo-β-1, 4-glucanase activity was restricted to the midgut, but the primary site of β-glucosidase activity was in the foregut and the midgut (Mac. barneyi). The functions of the gut segments apparently differentiated between feeding groups. The results suggest that the differentiation of feeding habits in flagellate-free termites was characterized by the distribution of cellulases in the gut rather than by variations in cellulase activity. PMID:23895662

Photosynthetic carbon fixation characteristics of fruiting structures of Brassica campestris L

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singal, H.R.; Sheoran, I.S.; Singh, R.

1987-04-01

Activities of key enzymes of the Calvin cycle and C/sub 4/ metabolism, rates of CO/sub 2/ fixation, and the initial products of photosynthetic /sup 14/CO/sub 2/ fixation were determined in the podwall, seed coat (fruiting structures), and the subtending leaf (leaf below a receme) of Brassica campestris L. cv Toria. Compared to activities of ribulose-1,5-bisphosphate carboxylase and other Calvin cycle enzymes, e.g. NADP-glyceraldehyde-3-phosphate-dehydrogenase and ribulose-5-phosphate kinase, the activities of phosphoenol pyruvate carboxylase and other enzymes of C/sub 4/ metabolism, viz. NADP-malate dehydrogenase, NADP-malic enzyme, glutamate pyruvate transaminase, and glutamate oxaloacetate transaminase, were generally much higher in seed than in podwallmore » and leaf. Podwall and leaf were comparable to each other. Pulse-chase experiments showed that in seed the major product of /sup 14/CO/sub 2/ assimilation was malate (in short time), whereas in podwall and leaf, the label initially appeared in 3-PGA. With time, the label moved to sucrose. In contrast to legumes, Brassica pods were able to fix net CO/sub 2/ during light. However, respiratory losses were very high during the dark period.« less

Brassica vegetables as sources of epithionitriles: Novel secondary products formed during cooking.

PubMed

Hanschen, Franziska S; Kaufmann, Martin; Kupke, Franziska; Hackl, Thomas; Kroh, Lothar W; Rohn, Sascha; Schreiner, Monika

2018-04-15

The epithionitriles, 1-cyano-2,3-epithiopropane, in particular, and 1-cyano-3,4-epithiobutane, are important, but yet underestimated glucosinolate hydrolysis products that are released instead of the cancer preventative isothiocyanates in Brassica vegetables, such as cabbage, broccoli, or pak choi. Here, we characterized the reactivity of 1-cyano-2,3-epithiopropane under aqueous heat treatment conditions and compared our findings to those of the related epithionitriles 1-cyano-3,4-epithiobutane and 1-cyano-4,5-epithiopentane. In contrast to the other epithionitriles, 1-cyano-2,3-epithiopropane is highly reactive. As a result, 2-aminothiophene and dimeric 1,4-dithiane-2,5-diacetonitrile were identified as main products and a reaction mechanism is proposed. Formation of 2-aminothiophene was also observed in cooked white cabbage samples. Moreover, three novel compounds were identified as derivatives of the related epithionitriles. The results imply that apart from isothiocyanates, process-derived compounds should be considered in regards to cancer preventative Brassica vegetable related bioactivity. Copyright © 2017 Elsevier Ltd. All rights reserved.

GLS-Finder: A Platform for Fast Profiling of Glucosinolates in Brassica Vegetables.

PubMed

Sun, Jianghao; Zhang, Mengliang; Chen, Pei

2016-06-01

Mass spectrometry combined with related tandem techniques has become the most popular method for plant secondary metabolite characterization. We introduce a new strategy based on in-database searching, mass fragmentation behavior study, formula predicting for fast profiling of glucosinolates, a class of important compounds in brassica vegetables. A MATLAB script-based expert system computer program, "GLS-Finder", was developed. It is capable of qualitative and semi-quantitative analyses of glucosinolates in samples using data generated by ultrahigh-performance liquid chromatography-high-resolution accurate mass with multi-stage mass fragmentation (UHPLC-HRAM/MS(n)). A suite of bioinformatic tools was integrated into the "GLS-Finder" to perform raw data deconvolution, peak alignment, glucosinolate putative assignments, semi-quantitation, and unsupervised principal component analysis (PCA). GLS-Finder was successfully applied to identify intact glucosinolates in 49 commonly consumed Brassica vegetable samples in the United States. It is believed that this work introduces a new way of fast data processing and interpretation for qualitative and quantitative analyses of glucosinolates, where great efficacy was improved in comparison to identification manually.

Selenium treatment differentially affects sulfur metabolism in high and low glucosinolate producing cultivars of broccoli (Brassica oleracea L.).

PubMed

McKenzie, Marian J; Chen, Ronan K Y; Leung, Susanna; Joshi, Srishti; Rippon, Paula E; Joyce, Nigel I; McManus, Michael T

2017-12-01

The effect of selenium (Se) application on the sulfur (S)-rich glucosinolate (GSL)-containing plant, broccoli (Brassica oleracea L. var. italica) was examined with a view to producing germplasm with increased Se and GSL content for human health, and to understanding the influence of Se on the regulation of GSL production. Two cultivars differing in GSL content were compared. Increased Se application resulted in an increase in Se uptake in planta, but no significant change in total S or total GSL content in either cultivar. Also no significant change was observed in the activity of ATP sulfurylase (ATPS, EC 2.7.7.4) or O-acetylserine(thiol) lyase (OASTL, EC 2.5.1.47) with increased Se application. However, in the first investigation of APS kinase (APSK, EC 2.7.1.25) expression in response to Se fertilisation, an increase in transcript abundance of one variant of APS kinase 1 (BoAPSK1A) was observed in both cultivars, and an increase in BoAPSK2 transcript abundance was observed in the low GSL producing cultivar. A mechanism by which increased APSK transcription may provide a means of controlling the content of S-containing compounds, including GSLs, following Se uptake is proposed. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

PECTATE LYASE-LIKE 9 from Brassica campestris is associated with intine formation.

PubMed

Jiang, Jingjing; Yao, Lina; Yu, Youjian; Liang, Ying; Jiang, Jianxia; Ye, Nenghui; Miao, Ying; Cao, Jiashu

2014-12-01

Brassica campestris pectate lyase-like 9 (BcPLL9) was previously identified as a differentially expressed gene both in buds during late pollen developmental stage and in pistils during fertilization in Chinese cabbage. To characterize the gene's function, antisense-RNA lines of BcPLL9 (bcpll9) were constructed in Chinese cabbage. Self- and cross-fertilization experiments harvested half seed yields when bcpll9 lines were used as pollen donors. In vivo and in vitro pollen germination assays showed that nearly half of the pollen tubes in bcpll9 were irregular with shorter length and uneven surface. Aniline blue staining identified abnormal accumulation of a specific bright blue unknown material in the bcpll9 pollen portion. Scanning electron microscopy observation verified the abnormal outthrust material to be near the pollen germinal furrows. Transmission electron microscopy observation revealed the internal endintine layer was overdeveloped and predominantly occupied the intine. This abnormally formed intine likely induced the wavy structure and growth arrest of the pollen tube in half of the bcpll9 pollen grains, which resulted in less seed yields. Collectively, this study presented a novel PLL gene that has an important function in B. campestris intine formation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Physiological responses of emerald ash borer larvae to feeding on different ash species reveal putative resistance mechanisms and insect counter-adaptations.

PubMed

Rigsby, C M; Showalter, D N; Herms, D A; Koch, J L; Bonello, P; Cipollini, D

2015-07-01

Emerald ash borer, Agrilus planipennis Fairmaire, an Asian wood-boring beetle, has devastated ash (Fraxinus spp.) trees in North American forests and landscapes since its discovery there in 2002. In this study, we collected living larvae from EAB-resistant Manchurian ash (Fraxinus mandschurica), and susceptible white (Fraxinus americana) and green (Fraxinus pennsylvanica) ash hosts, and quantified the activity and production of selected detoxification, digestive, and antioxidant enzymes. We hypothesized that differences in larval physiology could be used to infer resistance mechanisms of ash. We found no differences in cytochrome P450, glutathione-S-transferase, carboxylesterase, sulfotransferase, and tryptic BApNAase activities between larvae feeding on different hosts. Despite this, Manchurian ash-fed larvae produced a single isozyme of low electrophoretic mobility that was not produced in white or green ash-fed larvae. Additionally, larvae feeding on white and green ash produced two serine protease isozymes of high electrophoretic mobility that were not observed in Manchurian ash-fed larvae. We also found lower activity of β-glucosidase and higher activities of monoamine oxidase, ortho-quinone reductase, catalase, superoxide dismutase, and glutathione reductase in Manchurian ash-fed larvae compared to larvae that had fed on susceptible ash. A single isozyme was detected for both catalase and superoxide dismutase in all larval groups. The activities of the quinone-protective and antioxidant enzymes are consistent with the resistance phenotype of the host species, with the highest activities measured in larvae feeding on resistant Manchurian ash. We conclude that larvae feeding on Manchurian ash could be under quinone and oxidative stress, suggesting these may be potential mechanisms of resistance of Manchurian ash to EAB larvae, and that quinone-protective and antioxidant enzymes are important counter-adaptations of larvae for dealing with these resistance

Improving Growth and Productivity of Oleiferous Brassicas under Changing Environment: Significance of Nitrogen and Sulphur Nutrition, and Underlying Mechanisms